D'Argo and Stark try to heal John, left with his head open on an operating table, while Scorpius attempts to avoid discovery. Zhaan makes a great personal sacrifice, while Jothee and Chiana commit an indiscretion.
Moya docks at a commerce station so the crew can spend some of the money they acquired from the depository. Disaster strikes however when the station is hit by a storm.
The crew work out a way of getting free from the other ship and out of the wormhole. Things become more complicated when their new 'friends' begin to sabotage Moya and Crichton picks up a transmission from Earth.
Stark accidentally sends himself, Crichton, Aeryn. D'Argo and Jool back in time where they alter the timeline and are forced to interfere further to restore it.
In need of supplies, Crichton lands his transport pod on a dying leviathan which is full of hungry cannibals and a scientist who has the ability to create clones.
Moya rendezvous with Talyn who is seriously damaged. They hide in the atmosphere of a planet to prevent the Peacekeepers from finding them. D'Argo and Rygel go down to the planet to find Chromextin, a drug that will help Talyn recover.
The crew of Moya start blacking out and missing portions of time. Pilot becomes inhabited by another entity who needs to 'taste' each crew member to determine if they too are being inhabited.
D'Argo injures Crichton, as Crichton lies in a coma/near death, he escapes into a highly animated world. It's Farscape, Chuck Jones/Loony Tunes style. Meanwhile D'Argo's actions create a crisis on Moya, which could destroy the Leviathan
Aeryn is devastated. She leaves Talyn, and grieves on a planet. Talyn's crew tries to help but she doesn't want their help. She spots someone who might be her father. But not all family reunions are joyous.
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.