Season 1 (Tales from a Parallel Universe)
Kai and a small group of other Brunnen-G warriors mount a last stand against His Merciful Shadow as their planet, Brunnis-2, is destroyed. In a final act of defiance, Kai crashes his ship into the control pod of His Shadow's flagship, the Foreshadow. He is killed by His Shadow, his memories are taken from him, and he is forced to serve as an undead assassin in the Divine Order.
Two thousand and eight years later, Stanley H. Tweedle is an assistant deputy backup courier for the Ostral-B heretics, a resistance group fighting against the Divine Order. After unknowingly leading His Divine Shadow to an Ostral-B outpost, resulting in its destruction, he is captured by the mercenaries Feppo and Smoor who extract information from him on the locations of other Ostral-B planets. They sell this information to the Divine Order, resulting in the deaths of billions. Stanley, subsequently captured by the Divine Order and after undergoing interrogation, is made a class-four security guard on the Cluster, the capital planet of the Divine Order and League of 20,000 Planets. After being reprimanded for insubordination and failing to turn himself in, he becomes a fugitive on the Cluster.
Zev Bellringer arrives on the Cluster as a prisoner and is sentenced to be turned into a love-slave, after failing to perform her wifely duties and assaulting her fiancé. Other prisoners, including a group of Ostral-B heretics and their leader, Thodin, are sentenced to be publicly executed. Thodin attempts to use an explosive device to free himself, but the device malfunctions and releases giant Cluster Lizards from containment, wreaking havoc across the Cluster. Thodin escapes and frees the other heretics, and reluctantly rescues the cannibal Giggerota. During Zev's transformation into a love-slave, she is attacked by a Cluster Lizard, turning her into a love-slave/Cluster Lizard hybrid. Before the brainwashing portion of the transformation begins, Zev frees herself and places the 790 droid in charge of her transformation in her place, causing the robot head to be programmed to be a love-slave. Upon seeing Zev, 790 immediately falls in love with her and pursues her as she escapes. His Shadow awakens Kai from cryostasis to protect the secret weapons laboratory.
Stanley and Zev meet up and make their way towards the secret weapons laboratory, where they find several Ostral-B heretics attempting to board a ship. They are pursued by Kai, who kills Thodin and chases the others into the ship. Inside, the heretics are attacked and killed by a Cluster Lizard. Before his death, one of the heretics releases a form of energy into Stanley.
Stanley, Zev, 790, and Giggerota reach the ship's bridge. The ship introduces itself as the Lexx, a machine–insect hybrid and "the most powerful weapon of destruction in the two universes", capable of destroying an entire planet in a single blast. The energy Stanley absorbed is revealed to be the key to the Lexx, making Stanley its captain. As Stanley instructs the Lexx to fly off the Cluster, they are cornered by Kai who throws Giggerota off the bridge. Before Kai can execute the others, he instead heads to the ship's hold to protect the Divine Predecessors who are being attacked by a Cluster Lizard. After saving them, Kai regains his memories from the brain of the Divine Predecessor who killed him, prompting him to turn against His Shadow. The Lexx is pursued and boarded by His Shadow, who attacks Kai for turning against him. Stanley and Zev distract His Shadow long enough for Kai to destroy him; his essence retreats from the ship as it travels through a portal into the Dark Zone. While traversing the portal, the Lexx's memory of His Shadow and its allegiance to him is wiped. The Lexx destroys the remnants of His Shadow's fleet that followed them through the portal. The three then begin searching the Dark Zone for a new home, away from His Shadow.
During their search, they encounter Kai's homeworld and explore it for insights into his past. Finding the planet abandoned, they are pursued by Giggerota who attempts to destroy the planet by disabling a series of towers that are keeping a dying star from becoming a supernova. The trio become separated from each other and discover the Time Prophet's prophecy of Kai destroying the insect civilization. Giggerota disables the towers, but the crew escapes aboard the Lexx without her. She and the planet are destroyed in the supernova.
After some time, the Lexx runs low on organic fuel and lands on the nearby planet of Klaagia to feed. The group discovers a group of psychotics obsessed with "pattern", a liquid made from organic material that parasites within their bodies feed on. Stan, Zev, and Kai inadvertently awaken the parasite queen, who attaches itself to the Lexx and pursues them off the planet. The Lexx fires on the planet and destroys it, using the meteors to kill the queen.
Meanwhile, Kai is running low on protoblood, which he needs to function in his undead state; protoblood can only be found on the Cluster. The group returns to the Cluster to find it abandoned, learning that the entire population of the League of 20,000 Planets was culled to feed and awaken the immense Giga Shadow, the last remaining insect. With help from a defecting priest of the Divine Order, they stall the Giga Shadow's awakening long enough for Kai to plant a baby Cluster Lizard inside of it. As the Lexx and its crew are almost destroyed, the Cluster Lizard reaches the Giga Shadow's brain and consumes it, killing the Giga Shadow. With a fresh supply of protoblood, the crew returns to the Dark Zone to search for a new home.
