After returning from the feuding realms of Gundalia and Neathia, Danma Kuusou and his companions continue their lives on Earth. Now, a year later, the virtual reality world of Bakugan Interspace has finally recovered from the alien invasion and has once again become a place for brawlers to gather and challenge themselves. It turns out, however, that whenever Danma's Bakugan, Pyrus Dragonoid, unleashes his might in battle, the Interspace experiences new disruptions. Unable to harness the incredible powers granted to him by Code Eve—the Bakugan Mother spirit—he struggles to maintain control over the Mechtogan contained within him. When it goes out of control, the mysterious mechanical entity wreaks havoc on the battlefield, attacking friends and foes alike. To make matters worse, Bakugan Interspace is at risk of being infiltrated again. An unknown mastermind is sending mutated Chaos Bakugan into the system in order to brainwash brawlers and take control of the virtual realm. In anticipation of the inevitable confrontation, Danma must find a way to keep the Mechtogan's destructive force at bay and rally the Battle Brawlers once again. [Written by MAL Rewrite]

In Thrace, Arion is taken from his mother Demeter by the god Hades. In the Underworld, Arion is trained to be a warrior. His training is driven by revenge: Arion was told that his mother's blindness was caused by Zeus and Zeus' death will remove the curse. Finally, Arion and Geedo (a huge ape-like creature who had become Arion's friend and companion) left the Underworld to find Zeus. Seneca, a small thief, makes off with Arion's sword and this leads Arion to his first encounter with the forces of Zeus, commanded by his daughter Athena. Arion is captured but is later set free by Lesfeena, Athena's mute serving girl. As Arion rejoins Geedo and Seneca (and worries about Lesfeena), the forces of Zeus and Poseidon face each other in battle. In the background sits the scheming Hades, and the calm Apollon who seems to have plans of his own.

Five supernatural factions have been fighting against each other for who knows how many centuries, with the beginning of Aquarian Age always in mind. Kyouta, soon begins to see visions of mystical girls fighting, except they do exist. Soon he and his girlfriend Yoriko become involved and the battle for Earth and Aquarian Age lies in their hands.

A sequel to Aki-Sora under a new name.