The crew must stop Scorpius's research on wormhole technology. The only way to stop him is to board the command carrier and figure a way to destroy it from within.
Crichton, now aboard a dying leviathan named Elac, encounters an alien named Sikozu who aids him in stopping the Grudeks who are intent on obtaining toubray (Leviathan neural cluster tissue).
The crew discovers how far Scorpius has fallen in the Peacekeeper ranks. They must find and activate all the probes to stop the magnetic storm on Arnesk, but someone doesn't want them stopped.
The crew is on the way to rendezvous with Moya. After ingesting a concoction of Noranti's they stop for a break on a planet. Rygel is captured and entombed in amber by raiders.
While Moya and her crew are resupplying on a generally xenophobic planet, Aeryn kills the next prefect, along with many bystanders and D'Argo, while under a strange form of suggestion.
The crew consume food, sharing amongst themselves. Although if not ingested by the same person, it becomes toxic. They must quickly find a cure or they'll die.
After accidentally returning to Earth, Crichton discovers he is in 1985 and he has altered the time line, causing his father to be scheduled to fly on the doomed shuttle 'Challenger'.