One day the player's character meets Dan Kuso, one of the Battle Brawlers, who teaches him the rules in a fight against Shuji. (you get a Serpenoid, a Juggernoid, and a Saurus that match the attribute you chose at the start of the game). After going to the local store and meeting Alice, who suggests the player should battle with other brawlers in the park to earn BP (Bakugan Points, the game's currency) a strange Bakugan called Leonidas falls from the sky, who is now the new best friend of the player. (Leonidas' attribute depends on what attribute you chose). Leonidas is an unknown and aggressive Bakugan that was created by all the hate and anger of the lost Bakugan trapped in the Doom Dimension. In several fights the player will meet a lot of people but at the same time a Darkus user, whose name is Marduk, decides to rule over all Bakugan together with Vladitor, another Bakugan that suddenly appears.

Right after Naga got the Silent Core, the seals that held Vladitor captive in the Doom Dimension suddenly broke and he escaped from the Doom Dimension. At the end of a tournament when Dan makes the player an official Bakugan Battle Brawler, Marduk is revealed to have allied with Hal G, Masquerade and Naga in order to defeat the Battle Brawlers and rule over the worlds and the Bakugan. The player must win the Ultimate Battle Tournament, defeating also Dan, Runo, Marucho, Julie, Shun, Masquerade, and a 1-on-1 showdown with Omega Leonidas and Battle Axe Vladitor. After the player wins, both Vladitor and Leonidas disappear, saying they have only little power left after the brawl. Later, the player discovers that Vladitor gave Leonidas his remaining power, saying he deserved it, leaving Leonidas to assume that Vladitor "wasn't all bad". The game ends with the player throwing Leonidas in the air shouting, "Bakugan brawl!".