Chiana discovers a datacam vid that reveals the murder of a previous Pilot aboard Moya. The crew is shocked to see one of their own in the Peacekeepers' firing squad... Aeryn. Crichton must intercede in the violence and confusion that overwhelm Aeryn and Pilot as both struggle to face their dark pasts.

When Moya is attacked by Halos-1, a hostile ship, the crew discovers that rather than being injured, they have all swapped minds. Zhaan, on a diplomatic mission to the alien ship, is the only one unaffected. The Halosians then plant an acidic weapon in Moya's neural cluster, so that not only is the crew in a state of bodily confusion, they must also deal with the acid burning through Moya's circuits.

A hostile beast on Moya attacks and poisons D'Argo. The crew must hunt down and capture the beast alive if Zhaan is to find the anti-venom and save D'Argo's life.

A brainwashed Aeryn and Rygel return from a Commerce Planet with a surprise for Chiana-two fellow Nebari to take her home and "mind cleanse" her as well. Chiana learns her brother, Nerri is still alive and now the head of the Nebari resistance movement.

Although Scorpius' neural chip has been removed, Crichton feels he has no reason to live - Aeryn is dead, his power of speech is gone, and the Scorpy clone remains in his mind. What's more, the crew of Moya discover they have more than just Crichton and Scorpius to deal with... lurking in the Medical Facility is a murderous Scarran.

While searching for a planet to heal the dying Zhaan, Moya collides and fuses with a small spacecraft, seriously injuring Moya and trapping both ships in a series of looping wormholes. Crichton and the captain of the other ship, Neeyala, soon realize that one of the ships must be sacrificed if any of them are to survive.

While at a Peacekeeper memorial, Crichton and the crew are pulled back in time into a great siege between Peacekeepers and the Venek Horde. As they try to stay alive and get back to their own time, they realize that every action changes the course of history-with devastating effects on the future.

Although Scorpius' neural chip has been removed, Crichton feels he has no reason to live - Aeryn is dead, his power of speech is gone, and the Scorpy clone remains in his mind. What's more, the crew of Moya discover they have more than just Crichton and Scorpius to deal with... lurking in the Medical Facility is a murderous Scarran.

While at a Peacekeeper memorial, Crichton and the crew are pulled back in time into a great siege between Peacekeepers and the Venek Horde. As they try to stay alive and get back to their own time, they realize that every action changes the course of history - with devastating effects on the future.

The Peacekeeper Retrieval Squad lead by Aeryn's mother, Xhalax Sun, traces Talyn to a Jungle Planet where the gunship is recuperating. When Crichton, Aeryn and Crais divert the squad away from the gunship, they surmise that Talyn might not be the Peacekeepers' only target. Aeryn realizes that the pursuit of Talyn will not stop until Xhalax is dead.

An Ancient - again taking the form of Crichton's father Jack - appears on Talyn and accuses Crichton of sharing wormhole stabilizing technology with the Charrids, a vicious race allied with the Scarrans. With a Scarran Dreadnought on the way, Jack must unlock the wormhole technology in Crichton's brain to build the ultimate weapon - but must first confront the evil Scorpius Clone in Crichton's mind.

D'Argo and Rygel meet with Scorpius and Braca to negotiate Crichton's safe passage onto the Command Carrier. As a safeguard against doublecrosses, Scorpius suggests that Crichton and Lt. Braca wear matching I-Yensch bracelets that synchronize their nerve impulses so they experience one another's pain. However, before the deal is completed, two heavily armed crazies burst in and hold up the diner.