After the final downfall of the rogue Bakugan Naga, peace was brought back to Vestroia. With the help of Danma Kuusou, his companion Pyrus Dragonoid, and other Battle Brawlers, the Infinity and Silent Cores were combined and the realm was recreated.

However, New Vestroia will not be given any respite as humanoid alien invaders, the Vestals, arrive and conquer the Bakugan world in one fell swoop. Armed with a fearsome machine capable of restricting Bakugan into their ball forms, they aim to enslave the race as a form of entertainment.

Now, the only force standing in their way is the Bakugan Battle Brawlers Resistance—a group of humans, Bakugan, and Vestals who oppose the idea of annihilating a sentient race. Led by Danma, they must venture into enemy-occupied New Vestroia and repel the invaders, to assure the survival of the entire world.