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.

The story begins with a young boy named Dan who has never lost a Bakugan match. While in a match against a bully Dan sees a vision of two Bakugan brawling. Is there more to the game than what the players think?

A mysterious Bakugan player named Masquerade, who is ranked at #1 on the list of Bakugan players, is stealing Bakugan from players worldwide. Dan makes an open challenge to Masquerade, and loses two of his Bakugan to this mysterious player, thanks to a Doom Card, which makes a Bakugan disappear forever. Dan is lucky enough to not lose Drago, but might if he loses to Masquerade again.

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.

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.

Dan and Runo meet for the first time, outside of the Bakugan website, and realize that they live in the same town. Dan drops his BakuPod, and Runo picks it up, noticing that Dan has battled Masquerade. She goes in his place, but ends up battling a boy named Tatsuya.

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 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.

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.

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.

Julie and her childhood friend, Billy, go one-on-one in a Bakugan battle. Although Julie's defeated by Billy, she's impressed with his skills and his Bakugan, "Cycloid." They make a great team, and Julie wishes she could befriend a talking Bakugan. Later, when Julie admits to herself how lonely she really is, the Bakugan Gorem appears. The two seem to be destined for each other.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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?

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

Learning that Webmaster Joe is at the hospital, Dan and the other head there. However, while heading for Joe's room, Drago gets lost.

Alice helps a little boy defeat his biggest rival.