Crichton and Chiana try to infiltrate a peacekeeper base to get some vital medicine for Aeryn. Crichton gets caught by Scorpius and imprisoned. He is tortured using a device called the 'Aurora Chair' which is able to look inside his mind and where Scorpius learns that Crichton has the secret to creating wormholes.
A peacekeeper ship is approaching Moya, so Crichton and Aeryn pose as peacekeeper officers on a secret mission while everyone else gets locked into cells to make the deception seem realistic. The peacekeepers that come aboard have some secret cargo. But when their secret cargo escapes, no one on board is safe.
When a Starburst goes badly wrong, Moya collides with a Nebari ship. On board is Durka, Rygel's former torturer, who has been mind cleansed and now serves the Nebari. Chiana, an attractive young rebel faces the same fate. Rygel takes it upon himself to take revenge on Durka and ends up undoing the cleansing and restoring him to his former, tyrannic incarnation.
Moya responds to a distress call from another pregnant Leviathan. On arrival at a planet they are contacted by a Delvian who informs them that the distress call was a deception. It was her way a getting Moya to come to them. The Delvians have a hidden agenda though. They want to forcefully take Zhaan's knowledge and learn how she overcame her insanity.
Crichton comes across the same conditions that initially created a wormhole. He leaves Moya in his module with Aeryn where he attempts to create a wormhole and return home. Although a wormhole forms it is unstable and the module gets damaged and he is forced to make an emergency landing on the planet to make repairs. On the planet he and Aeryn encounter a holographic message sent by Crais, offering rewards for: D'Argo, Zhaan and Rygel.
During routine searches for Peacekeeper beacons, D'Argo falls down a chute, destroys a Peacekeeper shield and gets ejected into open space. After being rescued D'Argo starts to think that everyone on Moya are members of his family. Moya, meanwhile, starts to alter the environmental conditions inside the ship so that it is hardly habitable for the crew. .
A peacekeeper beacon goes off and Moya has to land on an alien planet to prevent it's signal being intercepted and Moya being discovered. Crichton, D'Argo and Aeryn leave Moya and explore the planet in search of a substance that can be used to numb Moya's senses so the beacon can be removed. Crichton gets separated from the group and meets up with some inhabitants of the planet who hide him from the authorities.
The crew find an old abandoned peacekeeper ship adrift in space, on board they discover that Crais was there recently where he deposited a unit of techs to make repairs. Meanwhile Rygel learns that this was the ship where he was first held captive and starts getting paranoid. Things get even worse though when a group of fire breathing aliens show up.
A group of Tavleks come aboard for trade negotiations. Rygel takes a vitally important crystal from Moya to make himself seem wealthy. The Tavleks kidnap Rygel and take him down to the planet, leaving one of their wounded on board. Everyone goes to the surface to get him except Zhaan who stays on board to keep an eye on the Tavlek left behind.
The crew come across a ship that is molecularly de-stabilizing. D'Argo makes everyone bring it aboard when he discovers that there are Ilanics on board. Crichton goes on to the escape pod he gets a shock and starts experiencing strange visions of the future, firstly of himself and Matala, then of Moya's destruction.