In the parallel world of Vestroia, a power-hungry Bakugan, a small marble magnetic sphere which when thrown on a gate card turns into a highly strong and powerful warrior named Naga decides to absorb the energy of the two opposing cores that preserve the balance and peace in Vestroia. However he absorbed too much power and energy found within the Silent Core, the source of negative energy. The Infinity Core, the source of positive energy had been absorbed by Naga's twin sister, Wavern. Bakugan Battle Brawlers: New Vestroia revolves around Dan, Marucho, and Shun being called to the newly restored Vestroia, allying with three new brawlers named Mira, Ace, and Baron against the evil Vexos organization.
Angered by his defeat in Vestroia, King Zenoheld has commissioned Dr. Clay to construct the Bakugan Termination Machine that wipes out all Bakugan in a predetermined radius. However, the six attributes are needed to activate it. Meanwhile, Mira returns to earth to pay Dan, Marucho, Runo, Julie and Shun a visit. King Zenoheld then challenges the six ancient warriors to a battle for their attribute energy.
As Dan and Spectra continue their battle, and the self destruct sequence begins counting down, the rest of the six fighting bakugan are freed from their prisons. As Shun and Marucho are reuinted with Skyress and Preyas, the bakugan in Dan and Spectra's battle suddenly return to ball-like states, and the battle ends in a tie. But CyberHelios wants to continue fighting, even if the battle is over.
As the battle between Maxus Drago and Maxus Helios rages on, Mylene interrupts Hydron in his collection room by dragging him off. She explains that they are leaving New Vestroia. Hydron refuses at first, being afraid to face his father due to his failure to successfully occupy New Vestroia, but agrees to Mylene's plan to label Spectra as a traitor.
With Mira returned, and the Resistance reunited, Dan and the others head for Prince Hydron's sky palace to free Skyress, Tigrerra, Preyas, Gorem, and Hydranoid from captivity. But before they can even get close enough, Hydron activates another dimension controller, causing the bakugan to turn back into balls. Quickly thinking, Shun grabs Mira and Marucho and grapples onto the top of a rising elevator and to safety. Down below, Dan, Baron, and Ace are saved just in time by their bakugan. But before they can think of a way to get up to the palace, Spectra and Cyber Helios challenge them to a battle. As Dan and Drago struggle to fight back against the power Helois now possesses, Shun, Marucho, and Mira have managed to sneak into Hydron's throne room and discover the bronze statues of the five other Guardian Bakugan, just before meeting face to face with Prince Hydron himself...
Dan and Ace engage Mira and Gus in battle against their mechanical bakugan. During the battle, Mira seems to be purposely losing. Baron, Shun and Marucho have beaten the other Vexos and arrive in time to see Dan and Ace win, claiming the mechanical bakugan.(Baron beats Volt; Shun & Marucho beat Shadow & Mylene) Spectra is furious at Mira's betrayal, claiming that they have even stronger bakugan than the ones Gus and Mira used. Mira apologizes for betraying them, but they welcome her back into the group otherwise. They next head to the vexal palace to free all the original Guardian Bakugan.