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.

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.

Talyn draws dangerously close to a star, pulled by a mysterious force. Two alien beings appear on board: the timid Sierjna and her captor, Mu-Quillus. Mu-Quillus is responsible for the radiation pulses that are compelling Talyn to fly into the sun. Stark makes a pact with Sierjna to free her spirit from Mu-Quillus, but his quest puts the rest of the crew in peril.

Crichton predicts a wormhole's appearance near Moya, but just then a giant space plant captures the Leviathan. D'Argo attacks the plant in his ship, sending it into Moya's conduits, making it even more difficult to kill. Finally, an agent is found to repel the plant, but it exists only in Scorpius's cooling rods.

After correctly sensing that a wormhole is about to appear near Moya, Crichton is sucked down it! Inside, he is confronted by an interdimensional being intent on discovering why Crichton was entrusted with this knowledge. The alien sends Crichton through various "realities" of past events to illustrate the danger of misusing wormhole knowledge.

Scorpius takes Crichton, D'Argo and Rygel into an advanced training camp where students learn mental discipline. In the camp, D'Argo confronts Macton, the Peacekeeper who murdered D'Argo's wife, and then framed him for the crime. While Scorpius forces Crichton into torturous anti-Scarran training, D'Argo must face past demons... alone.

Moya's crew tracks Aeryn to a Scarran Border Station. She is imprisoned upon a freighter about to leave for Katratzi, a Scarran base. To keep the ship docked and under quarantine, Noranti gives Rygel a deadly, contagious disease. This gives the crew time to plan a rescue, but no one figures on the cunning and ruthlessness of Aeryn's captor.