Runo meets a new Bakugan named Aerogan, who asks to be her partner. Aerogan must prove himself against Wiseman and his henchmen.

Given a brief pardon by Barodius after his earlier failure, Ren hatches a plot with Zenet to regain possession of the Element.

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

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

The Brawlers head to face Masquerade in one final battle.

Dan is feeling down after losing Drago to Spectre in battle, so he goes into training to try and win back his Bakugan.

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

The Brawlers are having trouble finding the Infinity Core. When they learn that their location might be being broadcasted, they shut off their signal.

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

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

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

Marucho reveals that he secretly moved to Dan's neighborhood, and throws an elaborate welcome party. Masquerade makes a business offer with the famous pop band duo, Jenny and Jewels. The duo crash the welcome party, and challenge the Battle Brawlers.

While at an amusement park, Dan and Runo are invited onstage to assist a magician act by two brothers. Dan picks a card, and realizes it's a Doom Card. The brothers are working for Masquerade, and Dan and Runo get tricked into a battle.

Marucho and Runo realize that the combined powers of the Bakugan Brawlers are not enough to defeat Masquerade. Without Dan's knowledge, they visit Shun to try and get him to join. Shun's grandfather tries to get them to leave, but Shun makes a deal. If they win, he joins. If they lose, he'll walk away.

Dan and Marucho fight against the pop star duo, Jenny & Jewels. After a narrow victory, Drago tells the Brawlers about how the Bakugan came to Earth, and how a human entered the Bakugan world of Vestroia.

Dan, Marucho and Mira join together to form a resistance. Dan must prove himself in an extra trial when resistance leader Ace forces him to battle Percival.

Klaus, Chan-Lee, and Julio return to finish off the Brawlers. Dan, Runo, and Marucho take them on, but what will happen when Klaus uses Marucho's stolen Bakugan?

When Shun leaves the group, Alice chases after him. Meanwhile Dan goes to take on Masquerade alone.

The Brawlers finally meet Julie up close and personal, but the mood goes from happy to sad when they see what's happening in Vestroia. Julie and Shun fight with Julie's friend Billy, the 9th ranked Bakugan player, and her neighbor Komba, the 5th ranked Bakugan player, knowing they were tricked by Masquerade to take out Dan and the rest of the Brawlers.

Lured by an invitation to celebrate their world class rankings, five of the top ten Bakugan players gather at a mysterious mansion. There they meet Masquerade & the evil Bakugan "Naga". They're put under a spell to take Dan & the other Battle Brawlers out of the picture. Meanwhile, Alice confesses that she believes that her grandfather Michael is responsible for the destruction of Vestroia. They decide to take a look around Michael's lab to find evidence of what happened to him.

Alice becomes Masked Man to aid Dan and Drago, but they find Centorrior and Druman unexpectedly powerful. Undeterred, Dan and Masked Man formulate a strategy to overcome their foes.

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

After a quarrel between the Brawlers, they all go separate ways. Julie decides to pursue her friend Billy and try to save him from Masquerade's evil ways.

Alice realizes that she may have a connection with the mysterious Hal-G, but doesn't have the courage to tell the other Brawlers. Meanwhile, Dan recalls the last battle he had with Shun. Shun's mother gives Shun a Bakugan, "Skyress", to watch over him.

As the Brawlers face off against Mechtavius Destroyer in the battle to end all battles, Dragonoid Destroyer pulls a surprise maneuver.

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.

Masquerade has been destroying the Bakugans of kids all over the world, and the Brawlers have to put a stop to it. Reluctantly, Dan accompanies Runo and Marucho to Shun's house to recruit him one more, but find out he's joining Masquerade! Dan accepts the challenge of battle, and with Drago, fights against Shun and Masquerade.

Masquerade manipulates two boys, Kosuke and Takashi, into using his Doom Cards against the Bakugan Battle Brawlers. He promises that he'll reunite their friend Ai with her brother if they help him. Wanting to help their friend, they take the bait and soon run into Runo and Marucho, who are at the airport to pick up their website friend, Alice. Luckilly, Alice is skilled in the finer points of combination battle, and coaches her friends to victory. Alice has a secret, however, that might just ruin her friendship with the Brawlers.

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

When Marucho loses his Bakugan to Klaus, he and Runo give chase, and wind up in Masquerade's castle!

Julie is still upset about Billy's betrayal, but tries to put it behind her so she can support the other brawlers. Meanwhile, Shun tells them about a valley similar to Bakugan Valley. Everyone heads there but on the way it is revealed that Shun lied about it being similar, and it was all a ploy to try and see why Masquerade always knows where they are all the time. He tells them that there has to be someone spying on them. At the valley, the 3rd best Brawler Chan Lee appears and challenges Dan to a brawl.

Dan has a hard time adjusting to life without Drago. He ends up causing a schoolmate named Ryo to drop his computer and runs away, hurting Ryo's feelings. Masquerade takes advantage of Ryo's hurt feelings, and Ryo beats Dan in a battle. Dan finds Drago, and tries to make up with Ryo.

Masquerade teams up with a player with Rikimaru, by giving him a very special Bakugan. When Rikimaru and Dan battle, Drago ends up using a dangerous move to save himself and win the battle. Dan gets angry, and throws Drago into a river, cursing the day they met.

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

Code Eve, transports Dan, Drago, Barodius and Dharak to a middle dimension so the final battle can be fought. The winner will not only be endowed with mighty powers, but will also be crowned the ruler of Bakugan.

The Brawlers travel back in time with the help of Professor Worton in an attempt to undo the destruction caused by Mechtavius Destroyer.

Hydron discovers that a fellow prisoner is none other than Gus Grav, who was presumed dead.

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

A long time has passed since Mag Mel and Razenoid's defeat. Earth, New Vestroia, Vestal, and Neathia have been emptied of all the Chaos Bakugan. Everyone has returned home, including Spectra, Gus, Paige, Rafe, Taylean, and Trister.

After attacking Bakugan City, Mechtavius Destroyer invades New Vestroia. The Bakugan put up a brave fight but are no match for his strength.

While Spectra Phantom deceives the people of Vestal, Alice Gehabich briefly overcomes her fear of becoming Masquerade to battle Shadow Prove, whose victory destroys the Resistance’s transporter system and traps Dan’s group on Vestal.

Alice and Dr. Michael use the teleportation signature left behind by Shadow and Mylene to backtrack to the palace; Zenoheld continues his attack, forcing Spectra and Gus to retreat and come up with a plan to counter.

The Brawlers travel into the Aquos world to find Naga, where they encounter Bakugan named Tayghen and Hairadee.

When Spectre's new sidekick Gus runs into the Brawlers, he goes into battle with Dan to try and teach him a lesson.

Still desperately searching for Marucho, Shun travels to Beta City. But while there, he has to fight against the Vexos.

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.

The Brawlers continue to hide out from the Vexos in Marucho's mansion, when they are paid a surprise visit by Baron's sister Maron. Having already lost his Bakugan's Attribute Energy to the Vexos, Baron decides it is safe to take her out to see the sites.

When New Vestroia is invaded and it's residents enslaved, Dan and Drago must join together to battle the attackers.

Tensions form between the group of Brawlers when it is believed that one of them is a double agent.

Marucho watches Dan and the rest of the Bakugan Battle Brawlers Resistance become a close-knit team.

At Klaus' Mansion, Dan Kuso defeats Spectra Phantom in a fierce battle with the help of his friends and Drago’s newly gained power, while Spectra vows they will battle again.

Dan travels to a new virtual Bakugan world where kids from all over the planet can battle! He gives his new friend Jake a lesson in how to brawl.

Naga and his followers sow panic worldwide, but the Brawlers return. Wavern creates a force field around them using the Infinity Core, yet it collapses due to the core's intense heat.

The Brawlers divide to defend separate areas of the neighbourhood. Billy and Cycloid arrive to assist Julie and Gorem. Julie warns that Tricloid's arrival will bring Naga's malevolent influence.

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?

As Hal-G releases 5th Paladins, all seems hopeless until the Brawlers send their Bakugan to aid a wounded Drago. They destroy the 5th Paladins as Naga absorbs the 5th Paladins' energies. With the last of his power, Drago fires a brilliant burst of fire.

Dan goes in search of Gus for a rematch, but when they get down to the brawl Spectre arrives with a big surprise.

The Brawlers help Mira in her quest to find out the truth about what happened to her brother, but while investigating they discover a secret about her father.

Shun and Ace pair up to enter the Bakugan tournament, but they can't seem to get along. They may not be able to work together as a team when the battles commence.

Shun and Ace face a tough fight when Vexos unleash their new Bakugan. Meanwhile, Dan and the others race to find the dimension controller in order to free the Bakugan.

After realising they have to wait to return to New Vestroia, Dan and the Battle Brawlers decide to enjoy some R & R at an amusement park while they plan their next move.

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.

Spectre wants Dan's powerful Bakugan, so he challenges him to a winner takes all battle. Who will come out on top?

Dan and Baron mistakenly wander into Spectra's battle arena while looking for Shun, Ace and Marucho. Let the brawling begin!

Mira battles Spectra to decide if she will join forces with her brother and try to take over the world, however, Spectra has a surprise in store.

The gang have one last controller to destroy before all of the Bakugan can be freed - but could this be trap?

Dan and Ace face a showdown with Gus and Mira if they are to destroy Spectre and save the Bakugan, but Mira has a surprise in store for her old friends.

Prince Hydron wants Bakugan trophies and turns the Bakugan warriors into statues and holds them prisoner in his throne room. Can Dan save the day?

Prince Hydron rebels against Spectre when his subjects retreat from New Vestroia. Meanwhile, Marucho battles to rescue his Bakugan from his bronze prison.

Marucho faces a final test to rescue all the Bakugan from Prince Hydron's throne room and Drago discovers an awesome power that makes him travel with the Brawlers.

As King Zenoheld sends the Vexos to steal the Six Elemental Attributes, Baron Leltoy is defeated by Prince Hydron in battle, losing the Haos energy and racing to warn the Resistance before the others are targeted.