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!

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

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.

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.

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.

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.

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.

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. 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, happy to have her brother back.

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.

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.

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.

The Brawlers head to face Masquerade in one final battle.

Joe shows up after Dan defeats Julie, Marucho, and Runo for Wyvern 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 the Pyrus Ultimate Dragonoid, and Duel Hydranoid beats the Darkus Lord and evolves into the Darkus Alpha Hydranoid.

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 Nobilion: 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. Nobilion also mentioned that the Negative Energy has also created the evil hybrid Bakugan. Upon running into Centorrior and Druman again, Drago and Nobilion end up engaging them in battle. With Nobilion'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 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.

The return of Naga's Ventus/Aquos servant hybrid Hairadee has brought new troubles for Komba and Shun. While 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. Will the three of them be enough to take Naga's servant on?

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.