At the beginning of the game, a cutscene showing Hal-G celebrating the completion of the Silent Orb and stating that all Bakugan will bow to him appears.

On Earth, the player is seen being teased by Shuji and his younger brother, Akira, due to their passion for Bakugan, yet not knowing how to battle.

When the player wins their battle against Shuji, Dan tells them that they should compete in the Neo Challengers Tournament.

After the player visits the Bakugan Store, run by Alice, a Battle Brawler, they head back to the park when flashes of light spontaneously appear.

Dan tells the player to go to the park to learn about Battle Royales, as the next tournament is exclusively in that format.

After the player wins the tournament, a person named Marduk appears with his Guardian Bakugan, Vladitor.

A very similar occurrence happens in the Maximum Power tournament, with Shun, the Ventus Battle Brawler, telling the player to abandon Leonidas.

A cutscene reveals that Vladitor was released by Hal-G, Naga, and Masquerade to aid in their goals to rule over all Bakugan.

After the player wins and joins the group, Masquerade and Marduk appear to inform them that they are participating in the Ultimate Battle Tournament, with the Brawlers quickly realizing that it would spell disaster if either of them won.

Days later, the player heads to the park and reminisces about his time with Leonidas, before the same flashes of light as before appear again.

It is possible at that point to activate up to three Ability Cards in order to power-up the Bakugan or to change the battle rules.