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 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.

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 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?

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.

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.

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.

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!

Alice tells Klaus about what she did as Masquerade, and gets pulled into a battle to punish her for sending his Bakugan to the Doom Dimension while she had been Masquerade. However, Klaus was just trying to teach her a lesson, that everyone, and everything must work together in order to create harmony.

The Battle Brawlers have managed to unite each element together, and they are given the blessing as the six new warriors. Hal-G and Naga are still causing chaos over Vestroia though, and now they are attacking Earth with the help of the hybrid Bakugan (Taygen, Hairadee, Rabeeder, Tricloid, Centorrior, and Druman) leading their Bakugan armies. The Brawlers must figure out how to save both worlds. Help is on the way though. Chan Lee, Billy Gilbert, Komba O'Charlie, Julio Santana, and Klaus Von Hertzon lead every Bakugan players of the world when they have decided to give assistance. Once Naga starts attacking with negative energy, his minions get charged up to turn the tables against the Bakugan players. Joe contacts the Brawlers that Naga in the real world. Drago senses Wayvern is in trouble when he sends his minions to find the Infinity Core, so the Brawlers head back to take on Naga.

Wayvern puts up an energy shield around Wardington powered by the Infinity Core to hold off Naga and his troops. Meanwhile the Brawlers return and join in the battle to protect all of Earth and defeat Naga before he can join the two cores together. Failure means that both worlds will be destroyed. Jenny, Jewels, and Marucho protect the city via sea, where the Ventus/Aquos hybrid Tayghen has been creating tsunamis. The singing of Jenny and Jewels gets Bordington's fans to come out and cheer. Can Marucho, Jenny, and Jewels defeat Tayghen?

Naga's troops have finally infiltrated Wardington after two defeats. Alice discovers that Tricloid's sister Rabeeder is invading the town. Little does she know the one she trained, Christopher, will also get involved in the battle. Dan is informed that Hairadee, Centorrior, and Druman are also approaching the city following Tayghen and Tricloid's defeat. When it appears these two are being overpowered, Klaus arrives. The three soon realize all that Rabeeder is doing is being controlled by her worry for her sister Tricloid. Alice starts doubting herself but Christopher helps her. Hydranoid defeats Rabeeder and is reunited with Tricloid as both of them return to Vestroia.

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.

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?

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.

Dan tells Shun, Julie, and Marucho that he has yet to pass the test in the Doom Dimension and the only way to have Drago evolve he has to defeat his friends one by one. Julie first battles Dan and Dan wins. Then, he battles Marucho and wins again. Shun says he will battle Dan the next morning. Masquerade is in the Doom Dimension and is about to start a battle with Alice.

The Bakugan Battle Brawlers enter Vestroia and realize Vestroia has become a hybrid world where two elements are mixed together to make one element together. They enter the Ventus and Aquos world where they meet Tayghen and Hairadee: two Bakugan of both Ventus and Aquos elements. As they fight, they suddenly see the portal to the next hybrid world of Vestroia is closing and so they agree that Shun and Marucho are to stay in the Ventus and Aquos world to defeat the two Bakugan. The rest of the Bakugan team disappear through the portal into another dimension of Vestroia.

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.