Crichton and the crew are reunited on Moya. Crichton finds Aeryn suffering from Heat Delirium and under the care of Scorpius, who wants asylum aboard Moya. Soon after, a giant Lukythian ship appears nearby, and its Captain, Ullom, claims that Aeryn was recently part of a team that assassinated an important Lukythian leader. Ullom offers to heal Aeryn in return for information about the plot. While battling with the notion of trusting Scorpius, Crichton remains unaware that neither Aeryn nor Ullom is telling the whole truth.

Aeryn is being held captive aboard a Scarran freighter captained by Jenek, who's determined to find out if Aeryn's carrying Crichton's child. To discover the location of the Scarran base where Aeryn is being taken, Crichton and Scorpius travel through a wormhole to a mixed-up "unrealized reality" version of Moya. As the others wait for their return, pursuing Peacekeepers draw closer.

Scorpius takes Crichton, D'Argo and Rygel into an advanced training camp where students learn mental discipline. D'Argo is confronted with the arrival of Macton, the Peacekeeper who murdered D'Argo's wife, Lo'Laan, then framed him for the crime. When Scorpius forces Crichton into torturous anti-Scarran training, D'Argo must face the demons from his past... alone.

The crew travels through a wormhole to Earth, 1985, and Crichton finds he has somehow disastrously changed the course of time - his father Jack is now slated to fly the doomed Challenger mission. Lying low in Crichton's home town, the 'aliens' use the timely Halloween celebrations to remain (almost) anonymous, while Crichton tries to revert the timeline - in the process putting his younger self in mortal danger.

Crichton, Chiana and Rygel are reunited with D'Argo and Jool at an archaeological site run by Jool's people, the Interions. The purpose of the dig is to find a missing probe that might reverse the planet's dangerous atmospheric conditions. Peacekeepers led by Grayza land and capture the crew, and Crichton finds himself unable to fight back, mysteriously compelled to do Grayza's bidding.