During an experimental space mission, astronaut John Crichton, a man from our time, is hurled across a thousand galaxies to a completely alien world. In his quest to return to Earth, he finds himself aboard the leviathan, living starship "Moya" populated by escaping political prisoners from myriad alien cultures during a major alien conflict. Moya is capable thinking for herself, but is piloted by Pilot, who is organically attached to Moya. Crichton must rise to the challenge of surviving in a world he barely understands, keeping one step ahead of the pursuing Peacekeepers, a race of deadly mercenaries, and their leader Crais, who will stop at nothing to capture him.
Among the disparate alien refugees is D'Argo, a brutish Luxan warrior; Zhaan, a mystical, Delvian high priestess colored ethereal blue from her bald head to her toes; Rygel, 26-inches tall, who claims royal sovereignty over 600 billion subjects even though he was deposed over 250 years ago; Chiana, a quick-witted, gray-skinned sylph who wears very little and talks like a valley girl; and Officer Aeryn Sun, a front-line solider in the Peacekeeper corps who is forced to join the rebels. The refugees are also chased by the unspeakably evil Scorpius.