One day Dan prepares for a brawl against Akira at the park. However, he arrives to find that Shuji (Akira's older brother) is Dan's challenger. A battle ensues, and during the course of the battle Dan has a vision of a Dragonoid struggling with a Fear Ripper. The battle continues and Dan is victorious. Dragonoid starts to explain what's behind the scenes of Bakugan and from that point forward, all the Battle Brawlers realize that Bakugan was more than just a game.

It seems that a very gifted and mysterious Bakugan player named Masquerade has been stealing Bakugan from kids all around the world. When Dan hears about this through his friends on the web, he decides to put an end to it and challenges Masquerade to a battle, only to be interrupted by Shuji who has been eavesdropping on Dan to get his revenge, and only to lose again. Later, Masquerade and Dan meet up and the fight is on! But Masquerade has a secret weapon called a Doom Card, which sends its opponent to its final demise. Dan loses twice and if he loses again, his Bakugan, Dragonoid will be lost forever! 

Masquerade meets with a young Bakugan player named Rikimaru, by offering him a very special Bakugan. Across town, Dan begins training for his rematch with Masquerade. Drago is still unsure of Dan's motives, but decides to team up with him in the hopes that he can help rescue Vestroia, the home of all Bakugan. On the verge of winning with Rikimaru, Drago decides to ignore Dan's orders knowing that they could prove fatal. Drago uses a dangerous technique to risk himself & win the battle. Angry, Dan curses the day he ever met Drago & throws Drago in the river! 

Dan's having a hard time without Drago around. He causes a school friend named Ryo to drop his laptop & runs off in disbelief, leaving Ryo feeling sad. Later, Masquerade takes advantage of Ryo's feelings against Dan, challenging Dan to a brawl & wins! Dan finds Drago, they make amends with each other, and Dan attempts to reconcile with Ryo. But he's still under Masquerade's influence, and a second battle is on! Dan is able to beat Ryo. In the first, Drago breaks Masquerade's influence over Ryo. But we have not yet seen the last of Masquerade! 

Dan and Runo meet for the first time other than on the Bakugan website and are surprised that they actually live in the same town! Dan accidentally drops his BakuPod, and after he is gone, Runo notices it and picks it up. She sees that Dan has been challenged to a battle by Masquerade down by the river. She decides to go in his place, but ends up dueling against a boy named Tatsuya. 

In the amusement park Dan and Runo are having fun until Dan and Runo are called to a stage where Kenta and Kenji, the two act performers, tell them to pick a card. Dan makes a bad choice by picking up a Doom Card! Dan and Runo later know that the two brothers are working for Masquerade. After that Kenta and Kenji challenge Dan and Runo to a battle, and they can't decide who should go! Instead of doing single battles, the brothers propose a tag team battle, but can Dan and Runo work well together? At first, the battle does not seem to be going well for them, as the two are still arguing. However they manage to learn to work together and claim victory. At the end, the two argue again, only this time Dan wants to relax on the Ferris wheel and Runo wants more excitement on extreme mountain. During the argument Drago and Tigrerra comment that they should've seen this coming. 

Marucho reveals that he has secretly moved into Dan?s neighborhood and throws an elaborate welcoming bash. Elsewhere, the famous pop band duo, Jenny and Jewels are approached by Masquerade who makes them a business offer they can?t refuse. The pair crash Marucho?s welcoming party and face off against the Battle Brawlers. 

Jenny and Jewels seem to be in control of the battle, but Preyas unleashes his special ability which helps the Brawlers win. Later Drago tells his side of the story about what happened to Vestroia, and tells of a man who went to Vestroia by the name of Michael, who is later known as Dr. Michael Gehabich. 

Masquerade manipulates two boys, Kosuke and Takashi, into using his Doom cards against the Bakugan Battle Brawlers. He promises to reunite their friend Ai (Known as [M[1]ew] in the english dubbed version) with her brother if they help him. Wanting to help their friend, they take the bait and soon run into Runo and Marucho who are at the airport to pick up their Website pal Alice. Meanwhile, Dan gets lost and runs into Ai's brother who notices Drago. During the battle Runo and Marucho battle it out. Luckily Alice is skilled in the finer points of combination battle, and coaches her friends to victory. But Alice is fighting her own battle; she has a dark secret that will affect the future of her friends! 

Julie and her childhood friend, Billy, have a Bakugan battle. Billy overpowers Julie with his talking Bakugan - Cycloid, and then he tells Julie where he found him. Later, Julie finds a Bakugan known as Subterra Gorem who helps Julie win another battle against Billy. 

Marucho and Runo realize that the combined strength of the Battle Brawlers doesn?t match up to Masquerade?s power. Without Dan?s knowledge, they visit Shun to try and convince him to join the team. Shun?s Grandpa tries to send them away but Shun challenges them to a brawl. If Marucho and Runo beat him, then he?ll join. If not, he walks away? 

Alice realizes that she may have a connection to the mysterious Hal-G, but can?t work up the courage to tell the rest of the Brawlers. Meanwhile, Dan recalls the last battle that he had with Shun and we discover why Shun decided to leave the game for good. Shun's mother gives him a very special Bakugan, Skyress, to watch over him. 

Masquerade has been destroying kids? Bakugans all over the world and the Brawlers need to put a stop to it. Reluctantly, Dan joins Runo and Marucho in another attempt to recruit Shun. When they arrive at Shun's home, Masquerade is already there! They can?t believe that Shun is on Masquerade's side. Dan accepts their challenge and together with his Bakugan Drago, goes up against Shun and Masquerade. Will Shun send Drago to the Doom Dimension or will his old friendship with Dan convince him to turn on Masquerade? 

5 of the top 10 Bakugan players are invited to Masquerade's home. Naga places them all under a spell, and now the Brawlers must overcome the top players in the world to keep their Bakugan safe. Later the brawlers realize that Alice's grandfather is a scientist who recently disappeared six months ago, and who is the culprit of how the Bakugan first came to earth. 

In this episode the brawlers finally meet Julie, but their happy moment soon goes into darkness when they see what is happening in Vestroia. Julie and Shun have a battle with Julie's friend Billy, the 10th Ranked Bakugan player and her neighbor Komba, the 5th Ranked Bakugan player knowing that they were hired by Masquerade to finish off Dan and his friends. Will Julie be able to fight her friend? 

Julie fights with the sadness caused by the bitter betrayal of her childhood friend, Billy. At the same time, Julie and the other Brawlers must show their support for Dan as he accepts a challenge from the 3rd Ranked Bakugan Brawler Chan Lee. Will Dan come out on top, or will Drago slip into the Doom Dimension? 

Julie fights with the sadness caused by the bitter betrayal of her childhood friend, Billy. At the same time, Julie and the other Brawlers must show their support for Dan as he accepts a challenge from the 3rd Ranked Bakugan Brawler Chan Lee. Will Dan come out on top, or will Drago slip into the Doom Dimension? 

After losing his best friend to Klaus, Marucho pleads to Klaus for the return of his beloved Preyas. In a desperate attempt to get Preyas back, Marucho and Runo run through a portal, chasing after Klaus and entering inside Masquerade's evil lair. Inside Masquerade's castle, they learn about Bakugan evolution, the miracle of power increase. The brawlers soon find out that the Bakugan who holds the Infinity Core will be the ultimate Bakugan. Just when they think it's strange enough, Julio Santana, master of the Haos attribute and 4th ranked Bakugan Player in the world challenges them. Dan surprisingly joins in the battle alongside with Runo. Can Dan and Runo defeat Julio's trump combination with his Tentaclear or will their Bakugan bow down before Masquerade's evil powers? 

Marucho is still mourning over the lost of his Preyas as the Brawlers go their separate ways after an unexpected quarrel. Julie is still trying her best to get Billy back to his senses. Dan and Julie soon return to Germany after discovering the location of Billy. In a rematch between Billy and Julie, their friendship is tested to its limits as Masquerade joins in, promising to increase Billy's rank in the standings if he defeats Julie. Will Julie be able to help Billy overcome Masquerade's control or will Billy recklessly defeat Julie once again? 

A fight breaks up Shun from the group of Battle Brawlers. As Alice chases after Shun to remind him of his friends, Dan is only thinking about himself taking down Masquerade. Shun and Alice meet up with Komba, who once again challenges Shun to a brawl. In this rematch with Komba, Shun must learn to depend on his friends or end up as bratty as Komba. Can Shun overcome this obstacle or will he lose to Komba's Harpus? 

Under the orders of Masquerade, Klaus, Chan-Lee, and Julio have returned to finish off the Brawlers. This time, Dan, Runo, and Marucho must take them on. However, during their battle, Preyas makes an unexpected appearance... in Klaus' hands! Can Marucho overcome the betrayal of Preyas? Will he try to get Preyas back? Or will he lose to Klaus again? After their previous fight, the Brawlers are still selfishly brawling for their own motives. Can they work together? Or will they be beat one-by-one? 

The battle between Dan, Runo, Marucho and Klaus, Chan-Lee, Julio heats up as neither side is willing to give up. With the brawlers at a huge Bakugan disadvantage, can they catch up? But, Marucho is finally back in the game with the return of his beloved Preyas. Can he bring up their team work? With Drago on the verge of evolving, they just might have a chance against Klaus, Chan-Lee, and Julio. 

The brawlers track down Webmaster Joe, they soon find out that he's in a nearby hospital. Once they get to the hospital, Dan rushes to get to an elevator but unfortunately misses it! But as he was running, Drago fell out of Dan's pocket and into the elevator as soon as it closed! Dan gets lost looking for Drago, and when the brawlers can't find him, they decide to go find Joe on their own. As Dan continues his search for Drago, a boy in hospital pajamas appears with Drago, revealing himself to be Webmaster Joe! Dan immediately challenges Joe to a battle, thinking that Joe was working for Masquerade, and also accusing Joe of stealing Drago. They go to the hospital roof to battle but during the middle of the battle, Joe faints and is immediately brought to his hospital room. Later on, Joe wakes up and asks to be on Dan's team of brawlers, which the brawlers gladly accept. This episode also reveals that Naga has a twin sister named Wavern, who holds the Infinity Core. 

Alice helps a seven-year-old boy named Christopher defeat his rival Travis. 

The brawlers have reason to believe that one of them is working for Masquerade. As Dan and Runo follow Alice for questioning, Julie is following Shun around who is mysteriously taking his grandpa for a visit of the city thinking that Shun's grandpa is Hal-G. Is there really a spy among them or is it just a lie? Can they trust Joe's information? 

The brawlers are now preparing to confront Masquerade in one last battle. However, Masquerade is well prepared. After defeating 5 of the top 10 Bakugan players (Klaus Von Herzon, Chan Lee, Julio Santana, Komba O'Charlie, and Billy Gilbert) by sending all of their bakugan to the doom dimension, Masquerade's Hydranoid had evolved into Darkus Dual Hydranoid! The last hope against Masquerade's evil Hydranoid resides within the brawlers, but Runo decides to quit playing Bakugan fearing that she may lose all of her bakugan. But with Dan's help she is back in the game. Marucho, Julie and Alice refer to them as a good couple at the end of the show. Can they win? Ending with 'I'm coming for you Brawlers', this concludes the first season of Bakugan. 

The Battle Brawlers learn through Webmaster Joe (who was on a trip with his mother) that Masquerade has defeated the World's Top Bakugan players, so they try to come up with a strategy to beat him. The strategy seems to backfire when Masquerade visits Dan's house and gets him to accept a battle. Now the evolved Drago and the evolved Hydranoid will go head-to-head. Completely taking down Drago, Masquerade commands Hydranoid to send Drago to the Doom Dimension. When Drago gets sucked in, Dan goes after him and runs toward the portal. Shun tries to stop him, but is too late. The Episode ends with the rest of them crying out for Dan. 

The Brawlers mourn over the loss of Dan and Drago. Meanwhile, Shun gets a challenge from Masquerade and decides to join Dan in the Doom Dimension. When Skyress learns of this plan, she tries to gather the other Bakugan and try to save Vestroia without putting their human partners in risk. Soon, the other Brawlers catch onto his plan and decide to join him, but first Runo makes a promise to Dan's mom - he's safe and will be home soon. 

In the Doom Dimension, the Legendary Ancient Warriors of Vestroia prepare to test the powers of the Brawlers, seeing if they are worthy enough to save Vestroia. The Brawlers are separated and Julie is left with Gorem to face the Subterra Warrior, Clayf, and a shadow of her perfect sister, Daisy. With help from Gorem, Julie learns that she isn't her sister and she can only do the best she can do. Because of this, Gorem evolves into Subterra Hammer Gorem, and defeats Clayf. 

Marucho must battle the Aquos Elemental Warrior, Frosch, and he is forced to send in Preyus early when he learns he is battling a shadow of himself. Preyus isn't feeling well throughout the battle, but he is able to give Marucho guidance to accepting his past. Marucho knew that he only did what his parents told him to make them happy, but he didn't like to always be so obidient. This causes Marucho to hate his old self. By accepting the past him, Marucho was able to help Preyus' digestion problem. This allows Preyus to evolve by spitting out his brothers: Aquos Angelo/Aquos Diablo Preyus. Will the combined strength of these brothers prove to be enough to defeat the Aquos Warrior? 

Shun is stuck with the female Ventus Lord, Oberus, who has summoned a child that looks like Shun's mom to battle. The child convinces Shun to play with her while the sun is still setting, which it never does. Shun must battle himself as well when he is forced to choose between going back or staying in this world with his mother. In the battle with Oberus, Shun believes that he doesn't need his friends. His belief causes Skyress to die after a great impact with Oberus. When Shun realises his mistake, a tear drops down onto Skyress' ability card, changing it, and miraculously reviving Skyress, causing her to evolve into Ventus Storm Skyress. 

Runo and Tigrerra must battle a young boy from Runo's past (a smaller version of Dan) summoned by the Haos lord, Lars Lion. The test is for Runo to realize how much she truly treasures her and Dan's friendship/love. When Tigrerra is getting hit by Lars Lion's piercing arrows of light, Runo realises the friendship/love that she treasures and says "We are Friends Forever Dan!" in the English dub, while she says "I love you Dan!" in the Japanese Version. When Runo realizes this, Tigrerra evolves into Haos Blade Tigrerra. 

Dan must battle the Pyrus Lord, Apollonir, in order for him and his friends to return to their world. He and Drago soon find out that they're battling a clown. Dan manages to win the battle, but Drago doesn't evolve. When Dan rips off the clown's mask, it turns out to be Runo. In order for Drago to evolve and Dan to past his test, he must battle, and win, against each of the Brawlers. 

Joe is determined to find out where his friends have gone, so he challenges Masquerade to a battle. At first Joe appears to be outmatched, but Wavern returns to give Joe assistance. The Brawlers also return, and Masquerade realizes his battle is only beginning. Dan explains everything about the Bakugan to his mother, who believes him and asks Drago to take care of him. Naga is revealed as one of the most dangerous Bakugan in the world. 

Dan tells Shun, Julie, and Marucho that he has yet to pass the test in the Doom Dimension and the only way to have Drago evolve he has to defeat his friends one by one. Julie first battles Dan and Dan wins. Then, he battles Marucho and wins again. Shun says he will battle Dan the next morning. Masquerade is in the Doom Dimension and is about to start a battle with Alice. 

Dan's final test is to beat his friends so his Dragonoid can evolve to the next level and become the Ultimate Bakugan. Dan battles Runo and Shun while Masquerade goes to see the Darkus Lord, Exedra, and he ends up fighting Alice as a mirage.

Joe shows up after Dan defeats Julie, Marucho, and Runo for Wavern to check out Drago's battling skills when Dan and Shun have their battle to finish Dan's test. Meanwhile, the Darkus Lord and Masquerade finish their battle. In the end Drago beats Skyress and becomes Pyrus Ultimate Dragonoid, and Dual Hydranoid beats the Darkus Lord and evolves into Darkus Alpha Hydranoid.

Alice is surrounded by fog, and finds out she's at the town where Dan lives. Runo finds her and tells her to get some rest and she asks her mom to look out for her. Meanwhile at Dan's house, all of the Brawlers, including Dans mother, watch the news about the strange weather happening around the world. While the the bakugan explain to Dans mother about the bakugan, Joe receives a message from Masquerade, asking him to brawl him again with his new Alpha Hydranoid. Dan decides he'll take over to fight Masquerade with Drago to end it once and for all with Masquerade. Dan wins and offers Masquerade to join the Battle Brawlers to help defeat Naga. But Masquerade refuses and takes off his mask. It is revealed that Alice was Masquerade the whole time! 

Hal-G appears to explain the origin of Alice and Masquerade. Because she is unable to forgive herself, Alice then disappears. Meanwhile a huge hole opens up in the ocean and weird weather has been happening all throughout the earth. Through much convincing, the Brawlers convince their parents about the Bakugan. What will they find in the decaying Vestroia? Dan and the Brawlers decide to take a little road trip, to Vestroia! 

Alice tells Klaus about what she did as Masquerade, and gets pulled into a battle to punish her for sending his Bakugan to the Doom Dimension while she had been Masquerade. However, Klaus was just trying to teach her a lesson, that everyone, and everything must work together in order to create harmony. 

The Bakugan Battle Brawlers enter Vestroia and realize Vestroia has become a hybrid world where two elements are mixed together to make one element together. They enter the Ventus and Aquos world where they meet Tayghen and Hairadee: two Bakugan of both Ventus and Aquos elements. As they fight, they suddenly see the portal to the next hybrid world of Vestroia is closing and so they agree that Shun and Marucho are to stay in the Ventus and Aquos world to defeat the two Bakugan. The rest of the Bakugan team disappear through the portal into another dimension of Vestroia. 

As the remaining Brawlers enter the hybrid world of Subterra and Haos, a pair of Subterra/Haos Bakugan sisters named Rabeeder and Tricloid fall in love with Dan. The sisters say the only way out is if they beat them in a race. Dan and Drago win and leave to the next world.

Dan and Drago enter the hybrid world of Pyrus and Darkus where the dark army is running rampant. Dan and Drago are saved from Pyrus/Darkus hybrid Bakugans Centorrior and Druman by Noble Lion: a Pyrus Tigrerra who is the oldest and wisest of all Bakugan. Nobilion explains how the negative energy has been influencing all of Vestroia, except those who can hide. Noble Lion also mentioned that the Negative Energy has also created the evil hybrid Bakugan. Upon running into Centorrior and Druman again, Drago and Noble Lion end up engaging them in battle. With Noble Lion's sacrifice, Dan and Drago try to defeat Centorrior and Druman. 

Alice arrives in Vestroia as Masquerade in order to help her friends. Masquerade finds Dan and he begins to help the weakened Dan and Drago. Centorrior and Druman though are able to counter sound judgment and all the power-ups that their Bakugan are given. Dan and Masquerade must work togerther to defeat Centorrior and Druman alongside an army of Serpenoids and Gargonoids. With Masquerade and Hydranoid using a cut and run trick, Dan and Drago lure them to the right spot where Hydranoid's attack manages to defeat Centorrior. Drago then uses his attack to defeat Druman. Masquerade then fades away encouraging Alice to continue on being a Bakugan Brawler and Alice obtains Hydranoid in the process. When the Brawlers reunite with each other, Centorrior and Druman watch from afar and stated that they are together just as Naga planned it to be. 

The Battle Brawlers have managed to unite each element together, and they are given the blessing as the six new warriors. Hal-G and Naga are still causing chaos over Vestroia though, and now they are attacking Earth with the help of the hybrid Bakugan (Taygen, Hairadee, Rabeeder, Tricloid, Centorrior, and Druman) leading their Bakugan armies. The Brawlers must figure out how to save both worlds. Help is on the way though, thanks to Joe. Chan Lee, Billy Gilbert, Komba O'Charlie, Julio Santana, and Klaus Von Hertzon lead every Bakugan players of the world when they have decided to give assistance. Once Naga starts attacking with negative energy, his minions get charged up to turn the tables against the Bakugan players. Joe contacts the Brawlers to alert them that Naga in the real world. Drago senses Wavern is in trouble when he sends his minions to find the Infinity Core, so the Brawlers head back to take on Naga. 

Wavern puts up an energy shield around Wardington powered by the Infinity Core to hold off Naga and his troops. Meanwhile the Brawlers return and join in the battle to protect all of Earth and defeat Naga before he can join the two cores together. Failure means that both worlds will be destroyed. Jenny, Jewels, and Marucho protect the city via sea, where the Ventus/Aquos hybrid Tayghen has been creating tsunamis. The singing of Jenny and Jewels gets Wardington's fans to come out and cheer. Can Marucho, Jenny, and Jewels defeat Tayghen? 

The battle against Naga's troops continues as Julie and Billy team-up to take on the Subterra/Haos hybrid Bakugan called Tricloid, who has been powered up by Naga negative energy. At first the two seem to be overpowered, but the adaption of each other's battle styles may be what's needed to help them realize how to work as a team again, especially when Naga decides to crash the party. Shuji and Akira also appear trying to get strategies from their sister Nene. With help from Nene and her Ravenoid, Gorem and Cycloid defeat Tricloid by getting rid of the Negative Energy that Naga placed on her. At the end, Julie asks Billy out on a date. 

Naga's troops have finally infiltrated Wardington after two defeats. Alice discovers that Tricloid's sister Rabeeder is invading the town. Little does she know the one she trained, Christopher, will also get involved in the battle. Dan is informed that Hairadee, Centorrior, and Druman are also approaching the city following Tayghen and Tricloid's defeat. When it appears these two are being overpowered, Klaus arrives. The three soon realize all that Rabeeder is doing is being controlled by her worry for her sister Tricloid. Alice starts doubting herself but Christopher helps her. Hydranoid defeats Rabeeder and is reunited with Tricloid as both of them return to Vestroia. 

The return of Naga's Ventus/Aquos servant hybrid Hairadee has brought new troubles for Komba and Shun. When Skyress is trapped in a barrier of ice, Shun reveals his ninja skills to free Skyress and defeat the hybrid. Julio crashes the party and helps the battle. Finally, Hairadee is defeated. Unfortunatly for Julio, he doesn't get any credit at all.

Dan and Runo stand as the only defenses against Centorrior and Druman. As Dan recalls his past battle with them, he realizes they don't have a chance without help. Julie, Billy, Marucho, Klaus, Julio, and Komba also get involved in the battle due to a transmission sent by Hal-G posing as Kato. Elsewhere. Alice stands ready to help her grandfather, who appears to have fully become himself again. She takes him to where Joe and Wavern are, only to find that she has been tricked! He unleashes Naga to take the Infinity Core but Shun, suspecting that Hal-G's transmission was a trap, turns up with Skyress to protect Wavern. When Joe gets captured, Chan-Lee frees him and joins the city's last line of defense by unleashing Fourtress. While Drago is stuck battling the last of Naga's servants, Wavern is in great distress. 

Wavern is calling to Drago to tell him that she needs help, while The top ranked Brawlers must defeat Centorrior and Druman. Naga's negative energy is proving to be too much for Wavern and Fourtress. With Centorrior defeated, the others deal with Druman as Dan and Drago head over to where Naga is. When Drago arrives, he fights Naga. With help from Julio, Runo has Tigrerra destroy Druman. Wavern asks Drago to attack her so she can give him the Infinity Core. He does so, and Wavern disappears. Drago becomes Infinity Drago. Drago then continues his fight with Naga. In an epic battle, the two seem evenly matched. However, Hal-G sends out his 5th Paladins to assist Naga. 

As Hal-G releases 5th Paladins, Naga is slowly recovering. All seems hopeless until the Brawlers send their Bakugan to aid a wounded Drago. They destroy the 5th Paladins as Naga absorbs the 5th Paladins' energies. With the last of his power, Drago fires a brilliant burst of light that Naga attempts to absorb. The Bakugan combine their power with Drago's and it proves too much for Naga, who overloads, unable to control the power and finally explodes, destroying Naga in the process. The Silent Core then merges with Drago. Now the time has come, and unfortunately all great things must eventually come to an end. After an emotional goodbye, a parting so emotional it brings tears to everyone's face, the Brawlers and the Bakugan part ways as a portal opens, and the Brawlers throw their Bakugan one last time. The Brawlers' Bakugan, along with the rest of the Bakugan on Earth enter the portal and return to Vestroia. Drago flies to the center of Vestroia with the soul of Wavern and restores the Silent Core and Infinity Core. Harmony is restored in Vestroia, and the six worlds merge into one peaceful Bakugan sanctuary. After Dan has a talk with a vision of a distant old friend, he meets up with Runo in the park and they pose in front of the camera before heading out on a date. 

The peace of New Vestroia does not last long. A race called the Vestals invade and colonize New Vestroia, turning the Bakugan back into ball form and making them their slaves for amusement, not knowing that Bakugan are intelligent creatures. One by one the six fighting Bakugan are captured leaving only Drago. Now the last hope for New Vestroia, Drago is separated from the core of Vestroia by the six legendary warriors, and heads to Earth to seek out his old friend Dan Kuso. The two leave for New Vestroia, with Marucho following after overhearing Neo Dragonoid's plan to leave the others behind. After they learn that the Vestals are responsible for capturing the bakugan after invading New Vestroia, Dan is confronted by Lync Volan and Volt Luster, two members of the Vexos, the top six brawlers among the Vestals. Just then, a girl named Mira, part of the Bakugan Brawlers Resistance, arrives and tells Dan of the new brawling style required for Bakugan battles. Dan manages to adapt to the new method quickly and wins two Bakugan from Lync and Volt. 

After the battle with Lync and Volt, Dan, Drago, and Marucho go with Mira to the Resistance base. Along the way, Mira reveals that only a few people of the Vestals realize that the Bakugan are intelligent creatures, while the rest of the people have not been told. She reveals that after discovering this for herself, and becoming outraged with her father for participating in the capturing of the Bakugan, she ran off and created the Bakugan Brawlers Resistance, joining with people who thought as she did. Upon arriving at the base, they meet Baron, a major fan of the Bakugan Battle Brawlers and the 6 hero bakugan. Shortly after, another Resistance Brawler named Ace, highly disapproves of Mira bringing humans to aid in their quest to free the Bakugan. Instead, he challenges Dan to a battle, and says that if he beats him, he and Marucho can join the Resistance in their quest to save the Bakugan. Dan gets off to a rocky start, but he and Ace are too evenly matched. With one win and one loss for each, their battle ends in a tie and they become fast friends. 

Now that Dan and Marucho are part of the Resistance, they gear up and get ready to fight back against the Vexos, first by heading for Alpha City and the Alpha dimension controller, one of the machines trapping Bakugan in their ball form, to take it down. To get themselves ready, Dan offers to train Baron, whom gladly agrees and can't wait for the lessons to begin but is afraid what will happen when Dan finds out that he was the one who lost Tigrerra to Spectra. But after Lync and Volt were defeated, Spectra Phantom sends out Mylene Pharoah and Shadow Probe to ensure that the Resistance is taken care of. The next day, in the middle of his training, Baron reveals he is discouraged after losing Tigrerra to Spectra in a battle, and says he isn't worthy of the lessons. Just then Mylene and Shadow crash land and Shadow is forced by Mylene to battle Baron. Baron is discouraged and is afraid of losing Nemus the way he lost Tigrerra. But, on the brink of losing Nemus for good, Baron pulls through and wins back three of Shadow's bakugan. 

Seeing how desperately he needs a partner to help Dan and the Resistance, Marucho takes his gear and heads out, in search of a Bakugan to battle with. At the same time, Mylene also goes hunting for Bakugan, after throwing away three she claimed useless. In the morning, Marucho meets Aquos Elfin, a Bakugan who turned out to know and have what might be a crush on Preyas. She explains that after his capture, she had to watch over the forest and protect the Bakugan living there from any harm. When Marucho asks to be partners with her, she at first declines because she claims to be "waiting for the right partner". But when Marucho explains that he needs her to help free the Bakugan (as this was what Preyas would have wanted) she says that if he passes her test, she will at least think about a "temporary partnership". As the testing goes underway, with Marucho not doing so well, Mylene flies over, and in fury, Elfin and Marucho demand she and the Vexos return the stolen Bakugan. Angered at how cruel Mylene is to the Bakugan she already carries (by throwing them away like trash), Marucho and Elfin challenge her to a brawl. Mylene, however, soon begins to show her skill and may end up winning Elfin as a new Bakugan. Just when Mylene is about to seize Elfin, a hooded figure wielding Ventus Bakugan arrives and saves Marucho. Mylene states that she's tired of losing to this hooded person and offers him to join the Vexos, but he leaves without saying a word and Mylene departs. Meanwhile, Marucho slowly awakens, despaired that Elfin was gone. But as it turned out, Elfin was merely off to find him some water, and then begins explaining how she couldn't let anything happen to her "goofy partner". In the end, Elfin and Marucho are partners, able to aid the Resistance in their journey. Later, in episode 6, the hooded figure's name is revealed. 

With the Vexos losing one by one, Gus Grav calls them all together to explain that the Resistance has to be defeated. So Gus decides to take matters in his own hands and confront the Resistance, and bring pride back to the Vexos. Meanwhile, the Resistance makes a stop en route to Alpha City, where Mira gives Dan a Bakugan Trap called Coin Scorpion to help in his battles. Not much is known about the Trap Bakugan except that they are incapable or unwilling to communicate. Excited, Dan takes off to get in some training with Scorpion. Just then, Gus shows up and starts to mess with Dan's head, asking what he will gain from saving the Bakugan, leaving Dan with this question. He returns later, asking Dan what the answer is to his earlier question, and it is revealed that he is the number two brawler among the Vexos. Feeling confident, Dan decides to take him on, but is soon overwhelmed with the power of Gus' Bakugan Subterra Primo Vulcan and loses but does not care. 

Prince Hydron is furious because he still needs Drago to complete his bakugan collection, so Gus challenges Dan to a battle in an effort to capture Drago. The Resistance is planning to attack Alpha City, but Mira wants to take a short detour to find her brother. During the ensuing argument, Ace seems and sounds like he is worried about Mira going somewhere that might be dangerous, which shows that he may have feelings for her. In the midst of the argument, Dan sneaks away with Drago to fight Gus and manages to battle well until Spectra joins in and Dan starts to struggle in the fight. Out of nowhere, Shun comes to his rescue. Shun beats Gus and Dan beats Spectra when Drago displays a massive power surge due to Helios' taunts about Tigrerra. Seeing that huge amount of power, Spectra shows a hint of betrayal when he says that he won't let the magnificent Bakugan become a play thing, meaning that he won't give it to Prince Hydron if he captures it. Back at the base, Shun explains that while he was in the mountains practicing ninja moves a portal opened up right in front of him and he got sucked through to New Vestroia. This is the reason why Dan couldn't get through to him back in episode 1 before Drago brought him to New Vestroia. After he rescues Ingram from the Vestals, she remained in his debt and the two banded together to free the Bakugan. As they make their way closer to Alpha City and the dimension controller, Dan asks Shun why he didn't reveal himself earlier when he rescued Marucho. Shun explains that he had something important to attend to. When they approach Alpha City, Shun reveals he will break into the city and find his Skyress. 

After Shun successfully leads the Resistance into Alpha City, Mira departs on her own mission: searching for her older brother, Keith. She heads to her home to search for clues on her brother's computer but comes up with nothing. After her father, Prof. Clay, arrives, she confronts him and he simply says that "he is no more." When she further questions him, he leaves for his lab, while Mira follows. Meanwhile, Shun takes the others to check out the control spire and they learn that the battles that take place in the arena below the controller are synchronized with the controller's power. At the lab, Mira witnesses the birth of the first cyber Bakugan: Ventus Altair. As the boys make their way to her location, Mira is confronted by Lync, who is armed with Altair. During the battle, Mira seems to have the upper hand with Wilda and her trap Baliton. That is until Lync activates two Double Abilities in a row. The scientists are worried about Altair's power fluctuation but Prof. Clay orders Lync to destroy Wilda and Baliton. Before he can, the massive overload causes Altair to crash and shut down, ending the battle. Prof. Clay decides to use the data to perfect Altair into the most powerful Bakugan ever. 

Ace and Shun team up in a Bakugan battle tournament in order to overload the dimension controller because it draws power from Bakugan battles. After Marucho is "purposely" disqualified in the singles round, he sneaks the others in. They almost get caught by some guards until Mira pretends to be a huge Vexos fan and they manage to slip away. As they remain hidden, the Vexos show up and Mira notices that Spectra tosses his Bakugan the same way as her lost brother Keith. Meanwhile, Ace and Shun are having trouble getting along in the battle tournament and are starting to lose against the Dark Angels who are Vexos wannabes. When their opponents begin taunting them, Shun and Ace put their differences aside and finally come up with a plan. They win with ease while claiming their opponent's bakugan. Shun and Ace prepare for their match against Lync and Volt. 

Shun and Ace have made it to the finals and they prepare to battle Lync and Volt. they were brawling with Altair and volt's new talking mechanical bakugan, Brontes. Meanwhile, Dan and the others head to the dimension controller but lose Marucho on the way. Things only get worse when they discover many other talking bakugan and then they are captured by guards who are marveled by the speaking Drago. Just then Marucho drops in and saves them. Things get worse for Shun and Ace when Lync combines his Ventus Altair with Ventus trap Wired and their bakugan traps, Hylash and Falconfly seem to have no effect. Shun and Ace discover Altair's weakness: it cannot sense multiple opponents and they manage to destroy it. While the others hold off the guards, Dan makes his way to the controller, finding that it is guarded by lasers. He throws Drago through the lasers and he hits the reverse switch, destroying the controller just as Shun and Ace defeat Lync and Volt. The newly freed bakugan rise up from the ground and everyone in the stadium learn the truth about the bakugan. 

As the Resistance heads to Beta city, there is a scene where that on both sides Dan and Runo miss each other dearly so Runo decides to go to New Vestroia to help Dan on defeeting the Vexos. After Keito flies her and Julie to Moscow to meet with Alice and her grandfather, Dr. Gehabich reveals that his transporter is not functioning properly and refuses to let Runo go. Later that night, Runo and Julie sneak into his lab and Julie prepares to send Runo off. Meanwhile, in New Vestroia, While they are having dinner Mira first hears about Runo from Dan and Questions him on if he and Runo were a couple (he says there not but Marucho says they are) and later that night everyone is beginning to hear their conversation because of the weakening wall between the two worlds. Runo does make it to New Vestroia but finds that she is only half way there, being unable to touch anything {she tries to hug Dan} but still able to see and speak with Dan. Prince Hydron decides to take advantage of Runo's distress by sending Shadow to make sure that Runo remains trapped. While Marucho handles Shadow, Dan takes Runo to the gate only to get attacked by Shadow's bakugan. With Dan down, Runo rushes to help him but he urges her to go to the gate. To make matters worse, Spectra, Gus and Lync follow her through the portal as do Dan, Mira and Baron. 

Dan, Runo, Mira and Baron make it to the human world but pick up some unwanted visitors in the form of Spectra, Gus, and Lync. Marucho manages to defeat Shadow and he, Shun and Ace decide to take out the Beta city controller to pass the time. Before Spectra takes his leave, he grabs Runo as a hostage and offers Dan an ultimatum: join the Vexos or risk Runo's safety. Dan, Julie, Baron and Mira split up and Dan and Julie run across Spectra and Runo. Mira chases after Gus to find Spectra and Baron fights Lync. Spectra reveals that he is actually against Prince Hydron's rule and wants to team up with Dan to take him down and in a show of good will, releases Runo. Mira's suspicion of Spectra being Keith only rise as she believes that he infiltrated the Vexos to free the bakugan. After Baron defeats Lync, we learn that Spectra and Gus only want to take down Hydron so that Spectra can succeed the role of ruler of the Vestals. Meanwhile, Dan refuses to believe Spectra intentions and before anything happens, Alice warps in using Masquerade's warp card. She takes Spectra and Gus (and Dan) back to the lab where Dr. Gehabich sends Spectra and Gus back to New Vestroia. Unfortunately, the transporter must be repaired before another trip can be made. So, Dan takes Runo, Julie, Mira and Baron to his house for the meantime. Lync crashes in but refuses Dan's hospitality but accepts Alice's, due to his hunger, after their ride leaves. Alice doesn't like Lync one bit and tells him that when the transporter is repaired, he is "so gone". Before the credits role, Lync is seen crying after Alice leaves him some food. 

Mira and Baron are stuck on Earth with Dan, Runo and Julie so Mira decides that they need to take a break so they go to an amusement park. Mira and Julie are separated from the rest of the group and run into Spectra and Gus who say that they came back to Earth by tracking down Dan's Gauntlet to the amusement park. Mira wants to know if Spectra is her brother Keith so she decides to brawl against him. However, Gus rearranges their little deal so she battles Gus instead. If she wins, Spectra takes off his mask but if she loses, she has to join the Vexos against Prince Hydron. At first Mira struggles against Gus' abilities, but with help from the original Subterra master Julie and her copycat ability card, Mira pulls through and defeats Gus. Despite Gus' attempts to dissuade Spectra, he removes his mask and is revealed to truly be Mira's brother Keith. 

While Mira and Baron help out at Runo's family's cafe, Ace, Shun and Marucho head to Beta City to shut down the controller, which has grown stronger due to Drago (and the Perfect Core's) absence. Hydron sends Mylene to deal with the resistance in Spectra's absence and states to himself that, when he returns, Spectra will find that the Vexos have a new leader. Later at night, Ace, Shun and Marucho hear the voices of Mira and Dan (respectively) and head out into the night, but it turns out that Shadow is the one making the fake voices. By the time Shun realizes it's a trap, Marucho and Ace fall for it. Ace wakes up in another place and finds Mylene. realizing that he has fallen for a trap. Ace begins struggling to defeat Mylene and her new attribute changing mechanical bakugan, Elico. In a flashback it is revealed that Ace is rumored to be a top brawler possibly stronger than the Vexos but refuses to enter tournaments. Mira confronts him and asks him to join her team. After he lost to her, she gave him Percival and he learned the truth about Bakugan. Meanwhile, in Ace's battle with Mylene, Ace becomes submerged in water and loses to Mylene. He does not arise, he is lost. 

Marucho finds himself in a desert with Elfin. After falling into quicksand, he is rescued by Volt who later engages him in a battle. Marucho seems to be doing well with his new trap, Tripod Epsilon but when Volt pulls out his mechanical trap, Dynamo, things get rough and Marucho is defeated and sunken in quicksand. Back on Earth, Mira and Baron hang out at Dan's, who after waking up from a dream, is still eager to return to New Vestroia in order to help Shun and Marucho. 

With Ace and Marucho captured by the Vexos, Shun decides to head to Beta City alone to destroy the controller. On the way, he is ambushed by Shadow Probe, who is armed with Darkus Hydranoid. In the middle of the battle, Shun and Ingram realize that it is not the same Hydranoid they know, it is really mechanical bakugan Darkus Hades. Darkus Hades was created from Hydranoid's DNA and has none of the weaknesses that Altair had. Shun tries his best to hold his ground but Ingram and Hylash are no match for Hades and Bakugan Trap Darkus Fortress. Shun contemplates throwing in the towel out of fear for losing his partner like how he almost lost Skyress in a tough battle, but Ingram convinces him otherwise and that she will always be there next to him. Shun is defeated by Shadow and passes out. The Vexos, having now captured the rest of the Resistance, plan to keep them as hostages while keeping Dan and the others stuck on Earth forever and while they take all Bakugan. 

Spectra and Gus, stuck on Earth, stay in an abandoned factory. When Gus returns with "juice in boxes",(there's no such thing asjuiceboxes on Vestal) he finds that Spectra is gone. While Dan trains Baron, Spectra runs into a fortune teller who tells him that if he stays on the path he's chosen than he will meet his end, but Spectra does not listen to her. Spectra decides to take Drago by force, now being tired of waiting for Dan to join him. He sends one of Gus' hornets to challenge him and they meet in the arena where he last fought Masquerade. Mira, Baron and Runo worry about Dan being out on his own. In the first round Dan takes a major loss, but manages to strike back with Pyrus Scorpion. But then Spectra pulls out his own mechanical Bakugan Trap Pyrus Multisided Metalfencer. Helios gets frustrated and demands that Spectra gives him more power. Spectra willingly obliges and activates a forbidden ability card to give Helios absolute power. Dan and Drago are disgusted by this massive power and what it could do to Helios, but neither Spectra nor Helios seem to care about the consequences. Drago is no match for this power and loses, with Spectra claiming him as his prize. Dan is crushed by his defeat and the loss of his partner while Spectra walks by the same fortune teller who is shocked by how much darker his future has become. Once again, Spectra does not care. 

Dan is upset about losing Drago but tries to move on and think of ways to get him back: starting with all out intensive training. Meanwhile on New Vestroia, Mylene wants to close to portal to keep Dan and the others on Earth, but Prince Hydron orders her not to, so as to allow Spectra and Gus time to return, which angers Mylene, who greatly enjoys her new power. Apollonir states that they must retrieve Drago as the Perfect Core is losing power and the other two dimension controllers are growing stronger. While training, Dan faints and develops a fever. He runs out into the park calling out to Drago, lamenting over how he lost Drago. All of a sudden, Apollonir shows up and to retrieve Drago, but Dan regrets to inform him that he lost Drago. Apollonir is disappointed that Dan has given up so easily and suggests that Drago is also upset at himself for losing the battle and letting Dan down. Dan wakes up, with his fever broken, to find that Apollonir has crossed over to Earth. Apollonir, linked to the Perfect Core like Drago, and is easily able to find Spectra and teleport everyone there. Spectra accepts Dan's challenge but brings out Helios to test if Apollonir is worthy of fighting Drago. Apollonir lectures Spectra on true Bakugan spirit but Spectra believes that power is the only way to win and brings out his Bakugan Trap Metalfencer. However, Apollonir easily takes them both down in one hit. Spectra finally sends out Drago, but Dan is shocked to see his friend has been altered in appearance while under Spectra's control. 

Dan, with the help of Apollonir, brawl against Drago, but Drago is not himself any more. Spectra has turned him into a corrupted black dragon. Dan tries to reach out to his friend, but it seems that Drago is unable to listen. Spectra uses the power of many forbidden cards to access Drago's Perfect Core abilities, but it puts Drago under mounds of stress. The legendary warriors conclude that Drago should not have been able to access the Perfect Core's power and change attribute while in his new body, but the power of the forbidden cards allows him to do so. Things look bad for Apollonir, as Drago seems unstoppable with all this power. Dan then notices that Drago is crying and that if he doesn't stop Spectra from giving Drago so much power, Drago could die. Apollonir believes that the only way to help Drago is to transform himself into pure energy and enter Drago's body to absorb the extra energy, however, Apollonir will not be able to attack or defend himself. Also, Dan must throw Apollonir into Drago's chest, but if he misses, Drago's condition could worsen and Dan may end up killing Drago and New Vestroia may turn back into six separate worlds. Dan successfully launches Apollonir into Drago's chest and Drago falls, defeated, returning to his normal self. Dan and Drago are happily reunited while Spectra does not seem that affected by the loss, and only insists that things will be different the next time they meet. 

The Resistance is ready to head back to New Vestroia and Dan wants to bring Runo, Julie and Alice along. But Mira suggests that they spend one last day for Dan to say goodbye to his parents. Alice uses her teleportation card and Lync convinces her to take him too, but he really just needs to meet up with Spectra and Gus. As Dan and the others meet Alice at the tower, Apollonir opens a portal to New Vestroia. However, they are ambushed by Spectra, Gus and Lync and to make matters worse, Mira betrays them and heads into the portal after explaining that Spectra is her brother. Dan and the others miss their chance and Apollonir is not strong enough to open another portal, so Alice takes them back to Russia to use her grandfather's transport machine. But, because Dr. Michael used the technology in Lync's Gauntlet to repair the machine and only those with Gauntlets can go through, meaning that Runo, Julie and Alice must stay behind. When Runo lies that she never really wanted to go to new vestroia and lashes out at Dan telling him to never come back he grabs her hands and says how hes sorry she's not coming and they gaze into each others eyes until the machine is ready he slowly lets her hands go. After that heartfelt goodbye with Runo, Dan, as well as Baron head through the transporter. 

As Dan and Baron safely make it back to New Vestroia, they find their base completely empty with no sign of Shun, Ace or Marucho anywhere. They discover that they are near Beta City and resolve to head there believing that Shun, Ace and Marucho have gone there. Meanwhile, as Spectra makes his return, the other Vexos are shocked to see that Mira is with him, saying that she has joined the Vexos. However, in her mind, she only wants to find out what Keith is really up to. Also, she discovers that Shun, Ace and Marucho have been captured and are being held hostage. She tries to release them. Dan and Baron sneak into Beta City and battle Mylene and Shadow. Meanwhile Mira is interrupted by Spectra who helps her release her friends, but he tells her that she owes him a debt. As the battle wages on, Baron is defeated defending Drago, who taps into the power of the Perfect Core, defeating Mylene and Shadow easily as well as destroying the dimension controller. Ace, Shun and Marucho reunite with Dan and Baron and they make their leave from Beta City. Later, Mylene accuses Spectra of her loss and the escape of the prisoners but Gus reminds her that she lost the battle, not him. Mira is still left wondering what her brother is up to. 

Mira is uncertain of her brother's intentions while in Gamma City. Meanwhile, Ace is unconvinced that Mira has betrayed them due to his feelings for her, but they all resolve to head to Gamma City for the final controller. That night, Spectra invites Mira to dinner where he asks her to join him because he needs her and cannot accomplish his goal without her. Mira is unsure and retires for the night. Later she contacts Spectra asking to battle him and let that decide her fate: if she loses, she will serve him but if she wins, he must go back to being her brother. However, after Helios has volunteered to become a cyborg bakugan after Prof. Clay had collected data on Drago while he was in Spectra's possession. Wilda and Baliton prove to be no match for Cyborg Helios and Mira loses. 

Mira and Spectra meet with Prince Hydron, who shows her his collection and later receives a message from his father, who is angered by the destruction of the other two controllers. Hydron then orders Mylene to divide and conquer the Resistance, since she has shown that they are weaker on their own and orders Lync to keep an eye on Spectra and make sure that his new mechanical bakugan is ready for battle. The Resistance arrives and Ace and Baron explain that the controller is underground and is the most powerful. They all head in but encounter Volt. Baron deals with Volt while the others proceed discovering that Gamma City is not a real city but a research facility. All of a sudden, Shadow and Mylene appear and Shun and Marucho step in to battle. Spectra takes Mira to see a team of special mechanical bakugan that he and Dr. Clay had designed themselves that were intended for Hydron but he intends to make certain that they only obey him. Spectra then orders Mira and Gus to use the bakugan to battle Dan and Ace to collect data on Drago and Percival. Meanwhile, the others gain the upper hand against the Vexos. Dan and Ace continue to the controller but encounter Gus and Mira. Ace is shocked that Mira has truly betrayed them and Gus orders Mira to prove that she is loyal to Spectra.

Dan and Ace engage Mira and Gus in battle against their mechanical bakugan. During the battle, Mira seems to be purposely losing. Baron, Shun and Marucho have beaten the other Vexos and arrive in time to see Dan and Ace win, claiming the mechanical Maxus Dragonoid traps.(Baron beats Volt; Shun & Marucho beat Shadow and Mylene). Spectra is furious at Mira's betrayal, claiming that they have even stronger bakugan than the ones Gus and Mira used. Mira apologizes for betraying the Resistance, but they welcome her back into the group otherwise. They next head to the Vestal Palace to free all the original Guardian Bakugan and save New Vestroia for good. 

With Mira returned, and the Resistance reunited, Dan and the others head for Prince Hydron's sky palace to free Skyress, Tigrerra, Preyas, Gorem, and Hydranoid from captivity. But before they can even get close enough, Hydron activates another dimension controller, causing the Bakugan to turn back into ball form. Quickly thinking, Shun grabs Mira and Marucho and grapples onto the top of a rising elevator and to safety. Down below, Dan, Baron, and Ace are saved just in time by their Bakugan. But before they can think of a way to get up to the palace, Spectra and Cyber Helios challenge them to a battle. As Dan and Drago struggle to fight back against the power Helios now possesses, Shun, Marucho, and Mira have managed to sneak into Hydron's throne room and discover the bronze statues of the five other Guardian Bakugan, just before meeting face to face with Prince Hydron himself. Meanwhile, Mylene, Volt, and Shadow order Dr. Clay to give them an escape off of New Vestroia, as the energy from the battle between Cyber Helios and Drago could destroy everything around them. Dr. Clay at first refuses saying that it would be treason, when Shadow reminds him he works for the Vexos now. Gus overhears their plan, but before he can warn Spectra, Lync hits him over the head and knocks him into a room, locking Gus inside so he can't tell Spectra of their plan. Back with Dan and Drago, Spectra, having underestimated the perfect core's power, has used the mechanical Bakugan he has to make Maxus Helios, a Bakugan who has all six attributes. Dan tries to use a combination of Ability Cards that tap into the Perfect Core's power, but still can't match Maxus Helios's power. Dan realizes he has no choice but to use the Bakugan he got from his battle with Mira to make Maxus Dragonoid, just as Spectra has again used the other six mechanical Bakugan on Helios. The two Bakugan face each other, preparing for the final battle. 

As the battle between Maxus Drago and Maxus Helios rages on, Mylene interrupts Hydron in his collection room by dragging him off. She explains that they are leaving New Vestroia. Hydron refuses at first, being afraid to face his father due to his failure to successfully occupy New Vestroia, but agrees to Mylene's plan to label Spectra as a traitor. Meanwhile, Mira, Marucho and Shun try to activate a machine to reverse the process of Preyas, Gorem, Tigrerra, Hydranoid and Skyress's petrification but are unable to determine the numeric code. Dan and Drago take to the skies to battle Spectra and Helios but the power coming from their battle is far too much and they crash into the palace. Mylene prepares for their departure from New Vestroia but not before tossing out Elico and Brontes, believing that Bakugan with feelings are useless and imperfect fighting machines, since Dr. Clay has already created many powerful mechanical Bakugan. Out of a stroke of luck, Elfin discovers the activation code, but with the palace self destruction under way it may be too late. 

As Dan and Spectra continue their battle, and the self destruct sequence begins counting down, the rest of the six fighting Bakugan are freed from their prisons. As Shun and Marucho are reuinted with Skyress and Preyas, the Bakugan in Dan and Spectra's battle suddenly return to ball-like states, and the battle ends in a tie. But CyberHelios wants to continue fighting, even if the battle is over. Cyber Helios and Drago engage just as Ace and Baron, riding on Percival and Nemus, meet up with Shun, Marucho, Mira, and the rest of the six fighting bakugan. As Cyber Helios and Drago battle, Spectra draws a blade, and forces Dan to battle him one on one. Before either battle can reach a conclusion, the Vestal palace explodes, barely giving Dan and Drago any time to escape as Spectra and Cyber Helios retreat with Gus, Brontes, and Elico (whom were thrown out of the escape craft by Mylene). Gus immediately informs Spectra that the others left New Vestroia to blame the occupation's failure entirely on Spectra's betrayal. Spectra merely states that he never really planned on returning to the Vestal home world anyways. Meanwhile, the Resistance celebrates their victory of liberating New Vestroia and freeing the bakugan. Mira, Ace, and Baron decide to return to their world to prevent the Vexos from ever returning to New Vestroia and enslaving the Bakugan again. The others decide to return to Earth with their Bakugan and the original fighting Bakugan, but Skyress declines the offer, saying that she can't bear to leave her home again and that Shun's future lies with Ingram. Right after Skyress leaves, Drago and Dan regrettably inform Marucho and the others that Drago cannot leave New Vestroia, as the Perfect Core is a part of him. But then Apollonir and the rest of the legendary soldiers appear and grant Drago freedom to live wherever he pleases, with the ability to go back and forth between the worlds as he wishes. With that, Dan, Marucho, Shun, and the rest of the Bakugan return to Earth. Various portals open up across the world, allowing Alice and Julie to reunite with their Bakugan. Dan arrives at Runo's family's cafe and tells her New Vestroia has been saved. Just as he believes Runo is about to run to him, she scoops up Tigrerra, reunited with her Bakugan as well. Highly embarrassed, Dan yells at Drago to never speak of this again. Marucho and Shun walk in with their respective Bakugan, and Julie joins the group shortly afterwards. The Bakugan Battle Brawlers are back together again. 

Angered by his defeat in Vestroia, King Zenoheld has commissioned Dr. Clay to construct the Bakugan Termination System, a machine that when used, kills all Bakugan in a predetermined radius. However, the six attributes are needed to activate it. Meanwhile, Mira returns to earth to pay Dan, Marucho, Runo, Julie and Shun a visit. King Zenoheld then challenges the six ancient warriors to a battle for their attribute energy. At first the six ancient warriors are doing great until Zenoheld combines his Mechanical Bakugan and easily overpowers the warriors. In a last ditch attempt, the ancient warriors vanish and summons Drago, Elfin, Ingram, Wilda, Nemus and Percival and their partners to give the six bakugan their attribute powers, causing them to evolve. Dan, Marucho, Shun and Mira wake up to find their Bakugan have truly evolved, and realize that New Vestroia is in danger. 

To obtain the Six Elemental Attributes, King Zenoheld has the Vexos search for the Bakugan Brawlers Resistance. Baron, after talking with Ace, decides to move out due to the lack of space in his home occupied by his giant family. While taking his siblings to the park, he runs into Prince Hydron who engages him in battle. All seems well when Nemus pulls out his attribute change ability, but he proves to be no match for Hydron's Subterra Dryoid. Mega Nemus loses the battle and the Haos energy. Baron must find a way to warn Dan and the others about the Vexos' return before they get targeted as well.

While Dan is shocked by a surprise visit from his father and Mira reminisces over Keith, Ace searches the city for a place Baron can stay. As he approaches a future building site for an apartments complex, Baron calls Ace and tells him how the Haos Energy was stolen by Hydron. Then Mylene appears and challenges Ace for the Darkus Energy. As the battle drags on Ace and Midnight Percival eventually become overwhelmed by her mechanical bakugan. Before Mylene can execute the final blow, Sirenoid appears from the lake below them, moments before Klaus, and joins Midnight Percival in battle. With their combined efforts, they manage to drive Mylene away, right after she says she will return with the rest of the Vexos for the Darkus Energy. It is revealed Klaus helped Dr. Michael develop his dimensional transporter system. After meeting up with Sirenoid, his foundation continues to fund the scientist's research as well as managing timeshare on Vestal. By the end of the episode, Baron had arrived to join them and Ace has become frustrated with Klaus's constantly calling him 'boy'.

Klaus, Baron and Ace successfully contact Dan and warn them about the Vexos, so Dan decides to head to Vestal and face the Vexos. However, when Zenoheld decides to test the BT system, Shun heads to New Vestroia with his newly evolved - and now male - Master Ingram, while the others head to Vestal. Once Shun arrives, he finds that all the Bakugan are missing and Master Ingram is still in ball form. Skyress arrives and tells him that a metal sphere came from the sky and sent a beam that trapped all the bakugan in ball form. Shun attempts to destroy the device but finds that it is protected by a force field. All of a sudden, Lync appears to take the Ventus energy and a battle ensues. When Master Ingram and Hylash have trouble against Lync's new mechanical bakugan, Shun is forced to call on Skyress for help. During the battle, Master Ingram begins feeling doubt about his evolution and is taken out of the battle. When Skyress begins struggling against Lync, Master Ingram decides to embrace his new powers and enters the battle, defeating Lync. In the aftermath, Skyress disappears and wishes Shun and Ingram luck.

Mira, Dan and Marucho head to Vestal to meet Klaus, Baron and Ace at Klaus' mansion. It is there Volt comes to retrieve the Pyrus energy after being humiliated by Prince Hydron. Volt and Dan are about to battle when Spectra and Gus appear out of nowhere. Gus attacks Volt psychologically by saying he stole Brontes' soul, as shown in the beginning of the episode when he forces Brontes, Elico, and Vulcan to evolve using a Forbidden Card. Volt backs away to let Spectra brawl Dan. Mira, Magma Wilda, Marucho and Elfin Version II join in the brawl to help Dan and Drago. Despite his friends being defeated,l Dan manages to beat Spectra using the power Drago received from Apollonir, despite Helios's upgrades. However, before Spectra leaves, he warns Dan that they will meet again.

Spectra makes a false appeal to the Vestals that he is the hero and is trying to stop Zenoheld from ruling all dimensions. On Vestal, Dan and the others purpose to stop whatever he is planning. Zenoheld and the Vexos realize that Spectra has stopped their ability to travel into Vestal by jamming their signals, so Zenoheld sends Shadow to earth to force Dan and the resistance to come to them. Shadow appears and frightens Alice until Chan Lee arrives and the three battle. Alice is initially hesitant to fight, as she might become Masquerade again, but eventually embraces the fearlessness of Masquerade and utterly destroys Shadow's Hades. However, Shadow then reveals his more powerful spider-like Bakugan and wins the battle in one turn. As a result of Darkus Fortress' attack, Dr. Michael's transporter system is destroyed leaving Dan and his friends trapped on Vestal. Meanwhile, Prince Hydron plans to travel to earth to lure Dan and his friends there.

After Alice's loss to Shadow, Alice teleports to Marucho's house to communicate with the Resistance at Klaus' house in New Vestroia. Alice warns them of the Vexos attack on her and that Runo and Julie could be next. Dan decides to head back to Earth, even though it is likely to be a trap. However, since Dr. Micheal's transporter was destroyed, they at first believe it is impossible for them to return to Earth. Luckily, Klaus has one of his own. As the Resistance heads to Baron's house so he can say goodbye to his family, Spectra appears in Klaus' mansion only to find the Resistance gone and leaves Klaus with a warning that they can't hide forever. When Spectra returns to his ship, he finds Gus has answered Volt's challenge for Brontes. A battle quickly ensue between the two and Volt tries his best to not attack Brontes directly, causing him to struggle against Gus. When Volt begins to predict Brontes' moves and gain the upper hand, Gus offers Volt a place beside Spectra, but he refuses. Unfortunately Volt is no match for his former partner, loses and passes out. Once Gus returns to Spectra's ship he says that Brontes has served his purpose and tosses him out like trash. Brontes lands on the ground, opens and cries out for Volt to save him.

The Brawlers return back to Earth and see Shun, Runo and Julie waiting for them. In order to evade the Vexos, everyone stays at Marucho's house equipped with a shield to hide the attribute energies' signal. Runo gets into a fight with Dan and thinks that he thinks that she's not strong enough to face the Vexos. Runo wanders out into the city hoping to draw in the Vexos, but Mira follows her and they are ambushed by Lync and Mylene. Things go bad and Mira loses her Subterra energy, making the Vexos one step closer to activating the BT System.

After Elfin overhears Preyas talking down about her receiving the energy and rash behavior, Elfin runs off into the city and encounters Shadow Prove and Hydron. Marucho and Preyas arrive in time to rescue her and a battle ensues. At first, Elfin and Preyas have trouble getting along but they put their differences aside and almost defeat the Vexos, but Elfin shields Preyas from an attack and therefore loses the Aquos energy. Preyas, out of anger for Elfin's sacrifice, easily defeats Hydron and Shadow Prove. After the battle Dan,Shun and Baron fell asleep. Everyone else did not know Elfin lost her Aqous energy. The Vexos need three more attribute energy's left.

Baron's little sister, Maron, uses Klaus' transporter to visit Baron, so Julie and Runo suggest to him to show her around town. Meanwhile, Shun sneaks away from Marucho's house an travels to the Samurai theme attraction in the same park that Baron and Maron are at. Shun encounters Volt disguised as a samurai and a battle ensues. At the same time, Baron activates his gauntlet to show Maron how it works and learns of Shun and Volt's battle. The two easily overpower Volt, keeping the Ventus energy safe. Maron bids farewell and thanks everyone for the great day and departs...not before thanking Shun for saving her and kissing him on the cheek.

Billy and Cycloid return to visit Julie only to find that she is at Marucho's house. On his way there, he is unknowingly followed by Mylene and Shadow. Meanwhile, Julie begins showing signs of interest in Ace after spying on him and Dan working out. After insisting she feels nothing for Billy anymore, Julie practically leaps into his arms when he arrives seconds later and introduces him to Mira, Ace and Baron. Billy is apparently caught up with everything happening after running into Klaus a while back and receiving a gauntlet from him. Not long after, Marucho's preparations for a virtual battle chamber called Bakugan Interspace are complete. The system allows anyone from all over the world play Bakugan like a game by logging on to the web. Everyone is eager to test out the machine, except for Shun, saying he has something important to take care of. Everyone draws straws to determine who goes first and Ace and Billy are chosen. Mira and Runo accidentally reveal Julie's crush on Ace to Billy and Ace, not wanting to come between the two, offers to take them both on, which they accept. As the battle rages on, Julie notices that Billy has become much stronger than before after easily defeating Percival. However, Ace easily counters back with the help of his newly evolved Trap Flash Falcon Fly. Meanwhile, Shun checks the security tapes and notices Shadow and Mylene following Billy to Marucho's house. Despite their advantage in numbers, Billy and Julie fall to Ace. After the battle, Shun urges them to return and shows them the picture of Mylene and Shadow from the security footage. Now knowing that the Vexos know where they are, they can no longer hide and wait. 

No longer able to hide from the Vexos, the brawlers realize they must now go on the offensive. They plan to storm the Mother Palace and directly attack the Bakugan Termination System instead of protecting the Attribute Energies. But without a working Dimensional Transport system or the coordinates to the Mother Palace, it at first seems there would be no way out for the brawlers. But Dan quickly realizes that they can find the location of the Mother Palace by convincing Spectra. The brawlers are hesistant, as Spectra will not likely be cooperative, and they have no way to contact him. Mira adds that there would be no way Keith would trust any of them. Meanwhile, the Vexos discover that someone has opened a portal to Earth from an entirely different universe. As Spectra makes his way to Earth, Dan and Drago admit how similar they are in both brawling abilities and lifestyles. When Runo interrupts the two for dinner, Dan and Drago are suddenly transported to Spectra's ship now that the former Vexos had broken through to Earth. Once there, Dan learns that Spectra needs the Perfect Core from Drago in order to make Helios the ultimate bakugan. They strike a deal: if Spectra loses, he will take the Resistance to the Mother Palace, but if Spectra wins, Dan must willingly surrender the Perfect Core to Spectra. During the battle Spectra realizes that the only way Helios can defeat Drago is by using his own natural abilities and powerful will to survive and evolve. Eventually Spectra's doubt in himself and his previous methods to perfect Helios leads to his defeat. Dan wins the fight and Spectra agrees to the terms of the bet. Everyone except Runo, Julie and Billy are transported to Spectra's ship, since he states that he would only allow the brawlers and bakugan originally bestowed with the Bakugan Attribute Energies to go with him. As Gus prepares the ship for the transport, Spectra thanks Dan for enlightening him, and refers to him as 'my friend'. Feeling humiliated after his defeat, Helios begs Spectra to make him even stronger. Spectra agrees, saying he will use the data he received on Bakugan evolution from an anonymous source to bring out new powers and new abilities from deep inside the Bakugan. 

Spectra upholds his part of the deal to Dan and takes the brawlers to the Vestal Palace, leaving them to find the BT System on their own. Spectra and Gus leave to confront Zenoheld and Spectra tells him to leave the brawlers be. Spectra leaves, but Gus later returns and challanges Zenoheld to a battle to avenge Spectra for being framed and betrayed by the Vexos. Gus' struggles in the battle become more obvious as both Elico and Hexados sacrifice themselves to protect Vulcan and Gus. In the final match, Vulcan protects Gus, saying that his loyalty to Gus knows no bounds like Gus' loyalty to Spectra. The two stand together and take Zenoheld's final hit and falls. It is unknown if he survived until episode 49 where he's seen inside a cell.  

The Resistance split up into groups to cover more ground of the Vestal palace. Shun and Baron encounter Mylene and Volt while Ace and Marucho face Shadow and Lync. At first it looks like things are going well but Dr. Clay uses the palace to send the Vexos' bakugan more power while lowering the power level of the Resistance. Shun and Ace are both defeated and lose the Darkus and Ventus attribute energies. As the others race to find Dan, he and Mira battle Hydron with the Pyrus attribute energy at stake, while Spectra presents a proposition to Dr. Clay.  

Spectra offers Dr. Clay a place by his side and the secret to Bakugan DNA, however, Dr. Clay remains loyal to Zenoheld and declares that he and Spectra are no longer father and son. A battle soon begins between Hydron and Dan and Mira, just as Spectra arrives to fight alongside Dan! Mira is quickly taken out just as the others arrive, too late to warn Dan about the Palace sending power to mechanical Bakugan. Spectra brings out his Battle Gear for Helios and easily takes down Hydron, prompting Zenoheld to enter battle. Despite their power together, Zenoheld overpowers them with a last resort power transfer and takes the Pyrus attribute energy, making the BT system fully operational. Unfortunately, Farbros is completely destroyed in the process. With the BT System fully active, the fate of New Vestroia's residents is grim. 

With the BT System fully armed, the Resistance and Spectra head to New Vestroia to initiate a mass evacuation. Many Bakugan are sent to Marucho's house on Earth including the Resistance's. However, Drago decides to remain behind to ensure that everyone has been rescued, remarking how many lives have been lost to protect New Vestroia such as Nobilion, Wavern dying, and also the six Ancient Warriors surrending their powers to six normal bakugan. Helios chases after Drago, refusing to allow Drago throw away his life while Helios still has a score to settle with Drago. Drago and Helios agree to destroy the BT System themselves. However, their powers are not enough. So, in a last attempt, Drago lifts the BT System from the ground and lifts it up to the atmosphere. Just as the BT System detonates, Drago hears Wavern's voice telling him to not give up and that he cannot die yet. Drago, given new determination, absorbs the attribute energies from the BT System and evolves while easily destroying the BT System. He returns to New Vestroia, greeted happily by everyone excluding Spectra and Helios. Mira questions Spectra on their terms of partnership, but Spectra declares he works alone. Spectra returns to his ship and leaves, but not before Helios declares his continuing rivalry with Drago. 

With the BT System destroyed and New Vestroia safe once more, the Bakugan are all moved back to New Vestroia from Marucho's house. The Bakugan thank the Resistance as they depart for Marucho's house while Klaus remains on Vestal in case the Vexos reveal themselves. Baron, Mira and Ace decided to stay on Earth to train and head to Dan's house for dinner. However, Marucho calls them saying that a strange ghost data has appeared in Bakugan Interspace in the form of unknown Bakugan. Everyone heads into Bakugan Interspace and meet four Bakugan that even Drago doesn't recognize! The Bakugan do not communicate, so Baron suggests battling with them. Marucho creates a digital copy of Baron so his challenger, Haos Aranaut, has a partner brawler. The battle does not go so well for Baron, and things get even worse when Avatar Baron whips out Battle Gear for Aranaut! Aranaut defeats Baron and Nemus and destroys the field of Bakugan Interspace. Everyone begins suspecting that Spectra may have sent the phantom data. 

While wondering where the Bakugan from Bakugan Interspace came from, Mira has just about given up hope on waiting for Spectra. Then, Spectra and Helios telepathically contact Dan and Drago to challenge them to one final match. Drago uses his Perfect Core powers to locate Spectra and teleport them to his location. The match begins and Drago appears to have the upper hand, that is until Helios whips out his Twin Destructor Battle Gear, which gives Drago a hard time. In their final fight, Drago calls on the power of his friends and defeats Helios. Spectra and Helios admit defeat and admit that Dan and Drago are the best brawlers. Drago didn't care about being number 1. Spectra decides to take off his mask and "work with the best rather than against him." Spectra becomes Keith again and Mira hugs him out of joy. 

While Keith has easily settled in as the newest member of the Resistance, with the exception of a jealous Ace. Due to failure, King Zenoheld abuses his son then Mylene tries to stand up for him. However, King Zenoheld rejects her until Hydron places the blame on Professor Clay. King Zenoheld agrees to pit the blame on Mira's dad. Professor Clay discovers the secrets of the DNA code as well as where the transmission originated from (possibly from Neathia). Meanwhile, Marucho analyzes the same data, as well as the one Keith received anonymously and discovers they are identical. Keith then suggests to construct Battle Gear for Drago. Drago denies at first, feeling it would be wrong being part machine but Keith assures him that the Battle Gear will be constructed from Drago's own DNA. This along with the lasting Vexos threat, Drago agrees, but must undergo a battle to test the virtual prototype. They enter Bakugan Interspace and Keith volunteers to use Ventus Hawktor and Subterra Coredem to battle Dan and Drago as Spectra! When Dan equips the gear, Drago struggles with it as his body is rejecting the Battle Gear. However, Drago continues to push forward and wins the battle, but nearly passes out due to the amount of power needed to control JetKor. Fortunately, enough data was gathered to construct Battle Gear that would not harm Drago's body. Shun and the other brawlers hope that Keith finishes Drago's battle gear before King Zenoheld and the Vexos do. The episode ends with Professor Clay telling King Zenoheld his ultimate weapon against the brawlers. King Zenoheld agrees with his research. 

Keith, Marucho and Mira work on constructing Drago's Battle Gear. However, Keith notices that Mira is distracted. Mira admits that she wishes their father would come around like Keith did so they could be a family. Keith doubts he will but offers Mira Gus' robotic bee to contact him. She does so and asks him to change sides, but Dr. Clay angrily refuses. Meanwhile, King Zenoheld changes his plan to destroy any living thing that stands in his way. Volt finds this plan goes too far and leaves the Vexos to return home while Mylene wishes him luck. However, his home is no longer what it used to be. Volt meets some children who still see him as their hero despite the things he did as a member of the Vexos and even promises to teach them how to brawl. As the children leave, Prince Hydron appears and a battle quickly follows and Volt easily takes the victory. Hydron is furious and throws a grenade that opens a dimensional port beneath Volt, sending him into a far dimension (possibly the Doom Dimension). As Volt sinks into the portal, he vows that Hydron will get what's coming to him for all the suffering he has caused innocent people. While JetKor has successfully been completed, King Zenoheld is glad to hear that Volt has been taken care of, he warns the others that they will suffer the same fate if they cross him. 

While the Resistance celebrate the success with Drago's Battle Gear, the Vexos begin to finish their plans for planetary domination. Lync, remembers how nice Alice was to him and worries that she may be one of the casualties. So, he copies the data for the Alternative System and heads to Moscow to give it to Alice. At first he hesitates, fearing that she may still be mad at him, but before he can make another move, Hydron appears and vows to destroy Lync. During the battle, Hydron implies that he wishes to leave the Vexos as well since he is mad that Lync has a choice to leave whereas he does not. Despite putting up a good fight, Lync is defeated and suffers the same fate as Volt. Before being completely dragged into the warp hole, Lync throws his glove with the chip inside in hopes that Alice will find it. After finishing cooking, Alice heads to find her grandfather and sees the results of Lync's battle with Hydron as well as finds his glove and the memory card. Alice gives the chip to her grandfather who insists they must show it to Dan and the others. When Keith asks how Alice found, she replied that Lync must have left it for her, but sadly adds that he may not be alive. Though the data suggests the Vexos Alternative System is incomplete, Keith states they will require the Bakugan DNA and Battle Gear data that they currently have, making them target for the Vexos once more. 

King Zenoheld sends Mylene to collect the Brawlers' Battle Gear and Bakugan DNA Data and Shadow Prove accompanies her. Having followed Billy to Marucho's house in episode 37, Mylene and Shadow have prior knowledge to their hiding place. Once they arrive, they are ambushed by the Resistance, but Mylene takes Mira hostage! Keith quickly agrees to give them the data in exchange for Mira but instead he leads them to Bakugan Interspace. Despite Mira's attempts to change Mylene and Shadow's mind, a battle quickly follows between the four. Shadow is quickly and effortlessly defeated by Keith and MAC Spyder is destroyed in the process. Mira soon defeats Mylene and destroys Macubass. Keith offers Myelene a place in the Resistance but she bitterly declines and throws one of Hydron's grenades. However, it results in a portal opening in Bakugan Interspace, further causing the Interspace to shut down...with the four of them still inside. 

King Zenoheld sends Mylene to collect the Brawlers' Battle Gear and Bakugan DNA Data and Shadow Prove accompanies her. Having followed Billy to Marucho's house in episode 37, Mylene and Shadow have prior knowledge to their hiding place. Once they arrive, they are ambushed by the Resistance, but Mylene takes Mira hostage! Keith quickly agrees to give them the data in exchange for Mira but instead he leads them to Bakugan Interspace. Despite Mira's attempts to change Mylene and Shadow's mind, a battle quickly follows between the four. Shadow is quickly and effortlessly defeated by Keith and MAC Spyder is destroyed in the process. Mira soon defeats Mylene and destroys Macubass. Keith offers Myelene a place in the Resistance but she bitterly declines and throws one of Hydron's grenades. However, it results in a portal opening in Bakugan Interspace, further causing the Interspace to shut down...with the four of them still inside. 

Hydron discovers that a fellow prisoner is none other than Gus Grav, who was presumed dead in episode 39. Meanwhile, Runo, Julie and Mira prepare a cake for Keith to officially celebrate his joining the Resistance. However, Keith's mind lingers elsewhere, something that Mira notices but Keith brushes off. Dan suggests that instead of waiting for Zenoheld's attack, they storm the palace. Keith, however, is too impatient and takes his ship to the Vest Palace on his own. A battle quickly ensues and Gus feels Spectra needs his help, so he tricks Hydron into battling so their bakugan can free them from their cells and Gus leaves to help Spectra while Hydron is left on his own. When Zenoheld nearly defeats Spectra, Gus arrives in the nick of time, shocking Spectra who is happy finding out that Gus had survived. Partway through the battle, Prof. Clay informs Zenoheld that the Alternative System, a giant airship modeled after Farbros, is complete and targets Spectra ad Helios for a test fire. The blast sends Spectra's ship flying and takes a huge chunk out of a small planetoid, Spectra and Gus just escaping the impact. Farbros links with the Alternative System and declares his quest for intergalactic domination to begin.