The peace of New Vestroia does not last long. A race called the Vestals invade and colonize New Vestroia, turning the Bakugan back into balls 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

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

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, 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

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

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 Scorpion to help in his battles

When Prince Hydron is furious because of his incomplete collection, Spectra and Gus challenge Dan to a battle in an effort to catch Drago. While the Resistance plans to attack Alpha City, Mira wants to take a short detour to find her brother. It is hinted in this episode that Ace starts to like Mira, during in the arugment, he seems and sounds like that he was worried about her going somewhere that might be dangerous

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, Dr

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 disquaified 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

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 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

As the Resistance heads to Beta city, Runo decides to go to New Vestroia to help Dan. After Kedo 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

Dan, Runo, Mira and Baron make it to the human world but pick up some unwanted visitors: 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 and Baron are stuck on Earth 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

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

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 trap, Dynamo, things get rough and Marucho is defeated

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 in disguise. Darkus Hades was created from Hydranoid's DNA and has none of the weaknesses that Altair had

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

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

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

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 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

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 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

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

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

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

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

Angered by his defeat in Vestroia, King Zenoheld has commissioned Dr. Clay to construct the Bakugan Termination System that wipes out all Bakugan in a predetermined radius. However, the six attributes are needed to activate it

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

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

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

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

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

After her loss to Shadow, Alice teleports to Marucho's house to communicate with the Resistance at Klaus' house. She 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

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 which is 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

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

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

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

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

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

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

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

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

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

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 to prove they are the best Bakugan team. Drago uses his new powers to locate Spectra and teleport them to his location

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

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

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

King Zenoheld sends Mylene and Shadow Prove to collect the Brawlers' Battle Gear and Bakugan DNA Data so with the data the Alternative could be finished faster. 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

With Bakugan Interspace beginning to collapse on itself, Mira and Keith attempt to save Mylene and Shadow, despite her wishes to die rather than face dishonorment. Before she can change her mind, she and Shadow fall into the Death Ball's portal while Mira and Keith are extracted from Bakugan Interspace safely. Meanwhile, King Zenoheld learns of Mylene and Shadow's fall and blames their lose, as well as the Resistance obtaining the Alternative data, on his son Prince Hydron who he has tortured as a result

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

With Keith having gone to the palace and having no way to find said palace, the Resistance are stuck. Luckily Alice and Dr. Michael arrive and use the teleportation signature left behind by Shadow and Mylene to back track to the palace

With the battle against the Alternative pressing on, Hydron shows up to lend a hand. Meanwhile, Prof. Clay receives a video transmisson from a faraway world just as Mira and Keith arrive to make one final appeal