A wormhole sends astronaut John Crichton to a distant part of the universe, where he finds himself aboard a living ship full of escaped prisoners. Captain Bialar Crais swears vengeance on Crichton when an accident leads to the death of his brother.
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.
Rygel is kidnapped by well-armed soldiers, who hold him for ransom. The crew must rescue him -- and Moya -- but soon succumb to the drug-induced effects of the Tavlek's weaponry.
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.
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.
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.
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 thief 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. But 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 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.
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.
