Aeryn has been critically wounded. She needs some tissue samples to heal. The only source is the Secret base the Peacekeeper mentioned. Crichton and Chiana go to the base, to get the samples. They encounter an old friend, and a new enemy.
Scorpius attempts to extract the wormhole technology from Crichton's mind, while Aeryn mounts a rescue operation. Crais finds himself at Scorpius' mercy, and Moya gives birth.
The crew find a planetoid that's a botanical paradise. Occupied by a scientist and a peaceful girl. But one is a killer. And there's more to this paradise than they realized. One of them wants Zhaan for their own agenda.
With death approaching in the form of Peacekeeper search parties, those aboard Moya say their final goodbyes, and share a last feast together, before enacting a plan to save Moya and her baby, named Talyn.
D'Argo takes part in a sacred ritual that helps an old Luxan, an Orican, to survive. During the ritual the Orican draws energy from who she thinks is D'Argo but is actually Moya. Consequently Moya starts to age rapidly.
A visitor comes on Moya with a device that could cloak Moya. The crew welcomes him on board, but soon almost everyone is acting paranoid, and the crew starts attacking each other.
Chiana discovers a recording with Moya's original Pilot. After seeing the recording and realizing Aeryn was involved, Pilot orders Aeryn to leave Moya.
Chiana is given a portrait in a store, which is more than it seems. The portrait changes and shows Chiana what will happen to her; when it shows she is on fire, the crew must discover the origin of the portrait, and they find an old enemy.
The crew needs food. Zhaan needs to eat meat and starts spewing spores. Only Aeryn seems to have a tolerance for the spores. While she's on Moya with Zhaan, the others find a Budong to get some food.
While waiting for Moya to pick their Transport Pod, Zhaan tells Crichton of Moya's adventures after the Gammak base was destroyed. Zhaan was on trial for murder, with Chiana and Rygel acting as her defense lawyers.
An alien ship fires a weapon at Moya. Although the energy shield is active, some of the blast makes it through and causes everyone's consciousness to jump into another body.
A strange globe appears on Moya, sucking in Crichton and duplicating him creating two additional people. One who is a de-evolved 'cave man' and another who has increased mental ability.
Look at the Princess finds Crichton, Aeryn, Rygel, D'Argo, and Chiana on a planet about to crown its new monarch. The problem is the Princess Katralla cannot ascend unless she finds a mate genetically compatible to her poisoned DNA.
Crichton has returned to Earth. Or has he always been on Earth all this time? People from his past and present appear. Is this some trick, if so who is behind it and why.
A temporal distortion traps Aeryn and John on a planet's surface, where they live out the rest of their lives - while Moya remains trapped in orbit, experiencing only hours. Stark returns to the ship with news of D'Argo's son.
A Nebari group come aboard Moya and attempt to mind cleanse everyone using a drug. Pilot and Rygel are the only two who can resist the effects. Crichton also remains unaffected due to Scorpius' neural clone.