To resupply the protoblood that sustains Kai's life, the crew of the Lexx travel back to the Cluster but find the planet deserted. The population was killed in "The Cleansing", in preparation of the birth of the Giga Shadow, the last survivor of the insect wars and sworn enemy of humanity. The crew try to destroy the Giga Shadow with the help of Yottskry (played by guest star Malcolm McDowell), a defecting priest of the Divine Order.

Fugitive security guard Stanley Tweedle, love slave Zev Bellringer, and love slave robot head 790 are thrown together by fate and on the run from His Divine Shadow after stealing The Lexx: the most powerful destructive force in two universes.

When an underwater ocean lab is lost in a earthquake, an advanced submarine is sent down to find it and encounters terrible danger.