The main conflict of the second season is the fight against Mantrid, the former Bio-Vizier of His Divine Shadow. The crew had inadvertently helped him transfer his mind into a machine in the first episode of the season while accidentally fusing it with a remnant of His Shadow. Mantrid's goal is to transform all matter in the Light Universe into Mantrid Drones.

In the meantime the crew keeps getting into difficult situations and is usually rescued by Kai. At the end of the season they destroy Mantrid. Unfortunately, the Light Universe is also destroyed. The crew flees into the Dark Zone.