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. In an effort to stop this, Drago is separated from the core of Vestroia by the six legendary warriors, and heads to Earth to seek out Dan Kuso, and the two leave for New Vestroia, with Marucho following after overhearing Drago's plan to leave the others behind. After they learn that the Vestals are responsible for the state New Vestroia has fallen into, he challenges Lync Volan and Volt Luster, two members of the Vexos. A Vestal named Mira, part of the Bakugan Brawlers Resistance, interrupts 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, 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 to battle Baron. After losing before, 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. But Mylene soon begins to show her skill, and may end up winning Elfin as a new Bakugan! just when all of mylene's bakugan were no use, she unleshed a bakugan called a bakugan trap. Just when Mylene is about to seize Elfin, a hooded figure wielding Ventus Bakugan arrives and saves Marucho. Mylene states 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, it is revealed that the hooded figure is Shun.

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. 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.

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. 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 hint of betrayal when he said 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 a portal opened up right in front of him and got sucked through 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 why Shun didn't reveal himself earlier when he rescued Marucho. Shun explains that he had something important to attend. When they approched Alpha City, Shun revealed he'd break in 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, Dr. 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: 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 Dr. Clay orders Lync to destroy Wilda and Baliton. Before he can, the massive overload causes Altair to crash and shut down, ending the battle. Dr. 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 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. As they remain hidden, the Vexos show up and Mira notices that Spectra tosses his Bakugan the same way as her lost brother Keith (later realize that Spectra might have somthing to do with the disappearance of 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 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 Wired and their bakugan traps 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, 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. Later that night, Runo and Julie sneak into his lab and Julie prepares to send Runo off. Meanwhile, in New Vestroia, 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 trys 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: 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 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 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 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. Back to Ace's battle with Mylene, Ace becomes submerged in water and loses to Mylene...and 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 trap, Dynamo, things get rough and Marucho is defeated. 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 in disguise. 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 by 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 he will always be there. 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.