First season[edit]
Stan, Zev and Kai accidentally steal the Lexx, the most powerful destructive weapon in the two universes. After successfully fleeing from the Cluster, the main planet of the
League of the 20,000 Planets, they are looking for a new home.
Kai needs protoblood to live outside of his cryochamber. Looking for protoblood, the Lexx returns to the Cluster to learn that a huge insect survived. This insect had controlled The Divine Order and His Divine Shadow in order to eat all human inhabitants of the 20,000 planets. The insect then begins a metamorphosis into the Gigashadow. Gigashadow produces protoblood. With the help of Zev, Kai manages to fill up his store of protoblood. Kai places the cluster lizard Squish in the brain of the insect and thus is able to destroy it.
Second season[edit]
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.
Third season[edit]
The Lexx is running out of food and must fly slowly to conserve energy. 790 computes that it might take thousands of years to reach an inhabited planet. The crew enters cryostasis to survive the voyage. After 4,000 years in cryostasis, they reach the twin planets Fire and Water. The entire third season takes place on these two planets.
The crew meets people they knew from the Light Universe. These survivors cannot remember their past in the parallel universe, though their personalities are still the same. Fire is ruled by the charismatic Prince. Water doesn't seem to have a ruler. The inhabitants of both planets live in isolated towns. On Water they live on islands in a huge ocean and on Fire there are big towers separated by desert.
Prince wants to win the crew over to his side, especially Xev. He tests their sense of morality through various temptations. The crew members are frequently separated, forcing them to act individually. After jumping from the Lexx to the surface of Water, Kai has trouble functioning normally without the other crew members. On Water, deep beneath its surface, Kai encounters his soul essence, which awaits rebirth. Stanley dies and a trial is held over the destination of his soul. All his bad decisions are weighted against his good deeds and he is sentenced to eternal punishment on Fire.
At the end of the season both planets, Fire and Water, are destroyed. Stan's soul is set free, and is able to return into his body, though he cannot remember what happened to him on Fire. The souls of all inhabitants of Fire and Water are also released, then travel to a planet that looks like Earth.
Fourth season[edit]
The Lexx travels to Earth looking for food. It is located in the very center of the Dark Universe and the crew assumes that it must be a very dangerous place. The crew again meet people they knew from the Light Universe, and from Fire and Water. Only Prince and Priest are able to remember their lives on Fire (though presumably Priest can do this only because Prince allows him to).
Kai's soul is stuck because he is undead, and he decides to die to release his soul. To do this, he must regain his mortality. He plays chess with Prince to regain mortality and wins, but remains undead.
The Earth is threatened by a being who resembles Lyekka. The crew finds out that the fake "Lyekka" destroyed all human life on her way through the Dark Zone. Kai decides to destroy the asteroid that is the source of the entity. Prince keeps his promise and restores Kai's mortality. Minutes later, Kai finally dies destroying the asteroid, saving all inhabitants of the Dark Zone. 790 destroys the Earth using the senile and dying Lexx. Prince, Priest, and Bunny escape on a rocket filled with Catholic schoolgirls, and Xev and Stan fly off together on the Lexx's offspring, "Little Lexx" to find a new home.