Alice appears to be disappearing all the time. Dan goes to talk with Marucho, Runo, Shun, and Julie and ends up finding Alice! Alice won't explain anything and leaves. Later, Joe receives a message from Masquerade, and 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!

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.

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.

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

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.

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 Hal-G doing a blurred transmission by Hal-G posing as Kato. Elsewhere Alice stands ready to help her grandfather, Hal-G, who appears to have fully become himself again. She takes him where Joe and Wayvern are. It's all a trick though. He unleashes Naga. Shun has suspected a trap though, so he shows up and fights Naga. When Joe gets captured, Chan-Lee frees him and joins the cities last line of defense by unleashing Fortress. While Drago is stuck battling the last of Naga's servants, Wayvern is in great distress.

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.

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 that wipes out 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.

The Brawlers have been pushed back, but will the return of Preyas and the evolution of Drago be enough to bring them to victory?

The Battle Brawlers learn through Webmaster Joe (who was on a trip with his mother) that Masqerade 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 with the loser getting a one-way trip to the Doom Dimension, which is later revealed to be full of Bakugan turned into stone.

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.

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.

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.

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.

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.

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.

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.

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. 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. In the brawl Dan manages to defeat Spectra after a three minute long battleand using the power Drago received from Apollonir, despite Helios's upgrades. However, before Spectra leaves, he warns Dan that they will meet again.

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 fall, dead.

The Brawlers head to face Masquerade in one final battle.