Crichton and Scorpius travel to one of the 'unrealized realities' where Crichton believes he heard Stark say "Katratzi." Meanwhile on a Scarran ship, Aeryn resists torture.
John Crichton struggles to learn the location of the mysterious Katratzi, whilst watching a television documentary about himself and the aliens.
The women of Moya travel to a dead Leviathan to buy a sensor beacon for Moya which will allow her to appear to be a different ship. While there Aeryn and Sikozu spy on a secret meeting between the Peacekeepers and the Scarrans.
The males of the crew undergo some training. Crichton learns how to resist Scarran probes. While D'Argo learns some self control D'Argo encounters his wife's murderer, his wife's brother.
Moya takes on a new passenger, Talikaa, when Chiana insists upon it. However Talikaa turns out to be an alien creature in disguise and is intent on harvesting the crew's neural energy.
Crichton has arrived home, on Earth. Even though the Moya crew relaxes, on Earth and are treated as VIPs, Crichton can't seem to adjust to life on Earth. After all his adventures, can he still call Earth his home?
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'.
Everyone finally reunites on Moya. But Aeryn returns with Scorpius, who claims to have saved the former Peacekeeper's life.
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.
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.
Everyone but Aeryn meets on Arnesk, where Jool has discovered the remains of an ancient civilization.
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).
Moya takes Talyn's remains to the sacred burial ground where D'Argo is forced to destroy a rogue Leviathan that is attacking other ships.
Crais gets Talyn to starburst inside the command carrier, causing it to collapse in on itself.
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.
Talyn gets the urge to fly into a sun. While in its vicinity Stark is contacted by an alien woman who is being held against her will.
Scorpius puts the neural chip into his own brain in an attempt to retrieve vital wormhole equations from Crichton.
Talyn lands on a planet covered mostly with vegetation that will help him to heal. Crichton, Aeryn and Crais leave the ship in search of Xhalax.
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.
Talyn is swallowed by a boodong, leaving Stark and Rygel stranded in a transport pod.