It's been several months since the crew disbanded, and Moya was sucked down a wormhole. Crichton is now on board an aged Leviathan, working on wormholes. But some visitors arrive who want to harvest the Leviathan. Crichton reunites with some of his old crew, and meets a new ally.
Everyone finally reunites on Moya. But Aeryn returns with Scorpius, who claims to have saved the former Peacekeeper's life. Aeryn forces them to accept Scorpius on board, and another crisis arises. Someone wants Aeryn for something she did while she was away from the rest of the crew. He promises a cure for Aeryn, if she'll co-operate. But Aeryn refuses. The crew must figure a ways to save Aeryn.
Pilot and Moya ask the crew to elect a Captain. They each take turns, a crisis arises when John finally summons a wormhole. Something attach itself to Moya. Aeryn's secret is revealed, but there's even more surprises. A leader will soon emerge.
Crichton and Chiana get stuck in a video game where they encounter strange/twisted versions of their friends. They must figure how to beat the game, or they'll be stuck inside forever. The game shows Crichton how dangerous/distracting his feelings for Aeryn are, leading him to a dark path to deal with his feelings
Bounty Hunters capture most of the crew. Only John and Noranti are free. Crichton must work with Scorpius to save the crew. When the bounty hunters shrink the crew, and hold them in containers on the bounty hunters, Crichton must figure a way to get rid of the hunters without harming the crew.
The crew gets checked out by a doctor for Space madness, a condition that's common in the area they're traveling. He gives them some food after the exam, and after they've ingested the meal, tells them the meal will cause them to get linked with whomever they split the dish with. D'Argo/Noranti, Aeryn/Rygel, and Crichton/Sikozu. He'll cure them ... for a price.
Crichton finds a wormhole, and studies with interest in his space suit, and gets pulled inside. He meets Einstein, and exposes Crichton to different realities to showcase the full potential of wormholes. Crichton realizes even his limited knowledge of wormholes is dangerous.
Crichton has returned to Earth, but it's the 80's. And Crichton's father is supposed to fly the ill fated Challenger mission. They must save his father, or everyone on Moya will never have met. And some secrets are revealed about John's past
Crichton has arrived home, on Earth. Even though the Moya crew relaxes, on Earth and are treated as VIPs, Crichton can't seem to adjust to life on Earth. After all his adventures, can he still call Earth his home?
The crew goes into Tormented Space, where they hope to avoid both the Peacekeepers and Scarrans. The crew buys maps for the area, Chiana buys a slave girl and sets her free. The crew tries to contact the trader after discovering Rygel cheated them. The crew starts acting stranger than ever. Rygel's greedier, D'Argo's angrier, Chiana's passion is on overdrive, etc. Crichton's behavior towards Aeryn are finally revealed.
The girls are out looking for an item that will camouflage Moya from long-range scans on an outpost in Tormented Space. While they are waiting for their part, they spot Braca and Grayza with a complement of Peacekeepers searching for them. They must lay low for 4 hours while they wait for their technology to be ready.
Aeryn has been captured by the Scarrans. The Scarrans realize they no longer need Crichton for wormhole technology. They can gain the knowledge from Aeryn's child. If the child is really Crichton's. More of the former peacekeeper's past is revealed as they probe her, and her grip on reality starts to waiver.
The crew has managed to rescue Aeryn, but Scorpius was captured. Fearing he might reveal wormhole technology to the Scarrans, the crew must rescue him. As the Peacekeepers, and Scarrans, negotiate a peace, Crichton offers some they all want to the highest bidder. Scorpius's allegiances are slowly revealing.
The Scarrans know where the Wormhole to Earth is, and they're on their way. Crichton and crew race to the wormhole to stop them. But saving the Earth means destroying the chance for John to ever return home. Aeryn finally reveals the father of the baby. John and Aeryn decide to get married, but fate steps in. The finale for the television series.