Beast Wars II tells the story of a battle waging between Lio Convoy's team of Cybertrons (Maximals) and Galvatron's army of Destrons (Predacons) on the planet Gaia. As Lio Convoy and Galvatron fight over the mysterious energy source known as Angolmois energy, many strange occurrences and mysterious properties of Angolmois begin to arise.

Although Lioconvoy managed to stop Galvatron's plans for exploiting the powerful Angorumoa energy, the Destrons refused to be deterred. Rallied by their new leader, the Destrons are attacking entire galactic quadrants in a hunt for the scattered capsules of Angorumoa. In response, the Cybertron elders appoint a powerful leader gather a team of heroes and stop the Destrons' plans. However, both sides of the conflict are being manipulated by the agents of Unicron, who desire the Angorumoa energy in order to revive their fallen master.