A sentient Ship with godlike powers (and aspirations) delivers the last survivors of humanity to a horrific, poisonous planet, Pandora-rife with deadly Nerve-Runners, Hooded Dashers, airborne jellyfish, and intelligent kelp. Chaplain/Psychiatrist Raja Lon Flattery is brought back out of hybernation to witness Ship's machinations as well as the schemes of human scientists manipulating the genetic structure of humanity.

The book deals with concepts such as artificial intelligence, worship, resource allocation, and religious violence. Clones and genetic engineering take up themes of racism. One of the major themes is leadership and how the values of leaders influence a society through the actions and narratives of a society's leaders. Another is the nature and definition of God. There are echoes of Herbert's exploration of the effect of greed on the leaders within a society and how greedy leaders will warp a society in order to consolidate their own power, a theme in the Dune books as well as The Dosadi Experiment (1977).

The book makes several references to Frankenstein, as an analogy to the relationship between Ship and humans. The book takes it a step further demanding that humans take responsibility for their creation by realizing Ship is a human artifact and its omnipotence ultimately sprang from human hands. This is what Ship meant when it demanded worShip.