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.

Mantrid versucht, die gesamte Materie, die im Universum der Lichts existiert, in einarmige „Mantrid-Drohnen“ umzuwandeln. Dabei ist er ziemlich erfolgreich, bis er am Ende von der Besatzung der Lexx besiegt wird. Allerdings wird dabei das Universum des Lichts komplett zerstört und die Lexx wird durch die dadurch entstehende Singularität in das alternative Dunkle Universum geschleudert.