Rygel and D'Argo meet with Scorpius and Braca to negotiate a deal, so the crew can board the command carrier. Two would-be robbers interrupt the bargaining process, now they're forced to work together to find a way out of their predicament.
The crew has been captured, Crais betrayed them. Now Scorpius is threatening Earth. Crichton must help him develop wormhole weapons or he'll wipe out Earth. Crichton has no choice but to help him. One person will make a decision that will stop Scropius's research, but a high price will be paid.
Moya wants Talyn's remains in a sacred Leviathan place. But another Leviathan won't allow it. The crew's last mission together is to help fulfill Moya's wishes. After that, everyone goes their separate ways. Crichton discovers a secret of Aeryn's.
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