John Crichton is an astronaut whose mission is to fly a module through the Earth's atmosphere and try to make the module gain speed. Something goes wrong and he is sucked through a wormhole. He is "saved" by some escaping prisoners and now has a race called peacekeepers chasing him.
Crichton finds himself on a world that has never encountered alien life before, and must enlist the help of a local scientist and her son to save Moya.
Alien life forms board Moya, and begin replicating the crew. Their problems escalate when a Peacekeeper squadron boards the ship.
Rygel is kidnapped by well-armed soldiers, who hold him for ransom. The crew must rescue him and Moya but soon succomb to the drug-induced effects of the Tavlek's weaponry.
Crichton jumps back in time over and over again, and discovers that a scientist who has come on board is hiding a dangerous secret.
D'Argo goes into Luxan hyper-rage, and the crew follows him to a worker planet. All is not as it seems, and John must avoid the natives' mind control to reveal a Peacekeeper plot.
Moya and her crew discover an abandoned Peacekeeper cruiser, with a sole technician on board. Aeryn and Crichton must defend the ship from a Shiang attack, while Rygel confronts a ghost from his past.
An evil wizard pits Crichton against Crais in a challenge to the death, and Zhaan embraces her submerged dark side to save her friends.
A geneticist offers the crew maps back to their own worlds -- but with a high price. Meanwhile, Aeryn Sun begins a bizarre metamorphosis.
Removing a Peacekeeper shield from Moya's internal systems blows D'Argo into space, and causes him to hallucinate about his past. Pilot also falls victim to mysterious changes in Moya.
D'Argo is captured and tortured by bounty hunters. Crichton and Aeryn must impersonate fellow bounty hunters in order to save him.
Moya finds a Delvian colony, where the inhabitants' lack of discipline are leading them to embrace their dark impulses. The crew struggle with hallucinations of people from their past, while Zhaan is betrayed by her people.
John and Aeryn are trapped in an energy net, and D'Argo must join forces with an irreputable pilot to rescue them.
Believing Moya has abandoned him, Crichton finds himself stranded on an alien world, and catches the eye of the daughter of the local ruler. When the crew finds him, Rygel is mistaken for the people's legendary savior.
The Nebari bring aboard a familiar face -- Captain Durka, Rygel's former captor and tormentor -- along with a theif named Chiana. Durka has been brain wiped and reformed, but his Nebari guide turns up dead.
Crichton finds a wormhole that returns him to Earth. When his alien friends are forced to follow, John must watch as the government imprisons and studies them.
A failed starburst attempt fragments Moya into different dimensions, and traps her. Crichton must travel between each dimension and find a way to free the ship.
Crichton impersonates a Peacekeeper captain when a PK commando unit boards the ship. But when their secret cargo escapes, no one on board is safe.
Crichton and Chiana infiltrate a Peacekeeper base to save Aeryn's life. When the base commander catches him and signals Captain Crais, Crichton learns that his brain contains the very thing for which he's been searching.
Scorpius attempts to extract the wormhole technology from Crichton's brain, while Aeryn mounts a rescue operation. Captain Crais finds himself at Scorpius' mercy, and Moya gives birth.
Hiding from Scorpius, the crew finds a world with a dangerous young woman and a scientist who isn't telling the whole truth.
Crichton and D'Argo embark on a suicide mission to destroy Scorpius' Gammack Base and allow Moya to escape. Scorpius forces Crais to make a bold move against the Peacekeepers.