Zev, Stan and 790 manage to steal the LEXX with the help of the rebel and make their escape from The Cluster. Thodin is killed by Kai who is being manipulated by His Shadow. But Kai retrieves his memory, learns his real identity and joins the crew of the LEXX. They ram through a fractal core anti-matter star into the Dark Zone where chaos, depravity and disorder rule, in their search for a new home.

Zev with help from 790s mega-memory banks, searches for Brunnis, Kai's long lost home planet, in order to find a way to keep him alive. Stan goes along reluctantly and Giggerota, the not-so-attractive cannibal, moves in for the kill but goes out with a bang.

The LEXX sets down on a garbage planet in order to feed. Stan, Zev and Kai make the mistake of getting out to look around. Stan is soon up to his neck, literally, in trouble and Zev is on the way to being liquefied but Kai saves the day.

Kai's time is up unless Zev can find a new supply of proto-blood to keep him alive. The only source is back at the Cluster, which is headquarters for His Shadow, evil ruler of the League of Twenty Thousand Planets. Stan wants no part of this near-suicide mission but Zev and Kai plunge in to do battle.

In this first episode, the crew encounters Mantrid, the former Bio-Vizier for His Divine Shadow. Mantrid claims he is able to provide the proto-blood necessary for Kai’s continued existence; but Mantrid, of course, has an ulterior motive. Mantrid is a brilliant but dangerous character who undergoes a transformation that makes him the main antagonist for the season.

Waking Kai can be a dangerous business, as Stanley Tweedle finds out the hard way. He is mortally wounded and rushed to the Medsat Medical Terminal where Doctor Kazzan saves his life. But the Doctor and his cronies have their own visions of power and glory and try to steal the LEXX to realize their nefarious dreams. Zev manages to foil their plans but in so doing makes the ultimate sacrifice, and loses her life while saving Kai and the others.