The crew are suspicious, and D'Argo, Zhaan and Stark come down to the planet to find out what has happened to Crichton. Although the chip has been removed from his head, there is still the Scorpius-entity present, though neither knows why. The Scorpius-entity tries to convince Crichton to die, to free them both. The rest revive the surgeon, who restores Crichton's speech, and puts his head back together. Crichton is encouraged to face down the Scorpius-entity, and manages to beat it. Back on Moya, Chianna and D'Argo's son do more than just prepare some food. Crais and Talon destroy a ship they think holds the real Scorpius and the chip, but they are mistaken. Meanwhile Zhaan finds Aeryn's body, and, by performing Unity, manages to revive her, but probably at the cost of her own life.
A storm hits a space station, damaging it badly, and trapping Moya in the dock. Zhaan is sickening badly. Aeryn saves a group of trapped children. Another space-storm is on its way, and D'Argo is needed to save Moya -- but he has just found out about Chianna and his son, and is feeling betrayed. Eventually, he goes out to untangle Moya, but is obviously suicidal. Chianna is frantic. Crichton manages to rescue D'Argo. D'Argo's son, feeling guilty, agrees to leave.
The crew are searching for a planet to regenerate a dying Zhaan. The last cryochamber contains a strange screaming female, Jool, who doesn't die, but is a bit miffed the others have. On the way, investigating a wormhole, Moya collides with a high-tech alien ship. Only one ship can be saved, and since Moya is too badly damaged, and Pilot comatose...
The aliens are systematically crippling Moya, to persuade her crew to save their own ship -- for if it is lost, all their families will be killed. When the crew discover this, they choose Moya. Even so, Zhaan has to sacrifice her life to free the others.
While viewing a famous war memorial, some of the crew are thrown back 500 years, to the events it commemorates, and upset the past. They are desperate to return the timeline to its original state before returning home. They nearly succeed.
Aeryn, Stark and Rygel discover a badly damages Tayln and a critically injured Crais. Meanwhile Crichton, D'Argo and Chiana are forced to land their pod in a strange Leviathan. There they discover a gruesome group of cannibals eating the ship and each other, a traumatised, half eaten Pilot, and a criminally insane monster duplicating people. He duplicates D'Argo, and one dies. He duplicates Chiana, and one dies. He duplicates Crichton, and both survive to return to Moya.
Crais recovers. The crew try to buy a vital substance to cure Tayln, but keep getting double crossed. Having two Crichtons is useful for fooling the lie-detecting critter. Aeryn discovers her mother is leading the Peacekeeper recovery team after Tayln. When the Peacekeepers turn up, Aeryn, Stark, Crais and one Crichton starburst away in a partially recovered Tayln, while the rest, including the other Crichton, flee in Moya.
Tayln, Crais, Aeryn and Crichton are swallowed by a giant space creature. Aeryn agrees to be hooked up to Tayln to help them escape. Tayln is jealous of Crichton, and makes him think Aeryn has "recreated" with Crais, then tries to space him. Aeryn convinces Tayln at the last minute to save Crichton. Stark and Rygel help Tayln's escape by feeding ice to the monster, to make it vomit.
Back on Moya, strange things start happening after passing through a nebula -- the crew discover they have "lost time". Then they find Pilot possessed -- by a creature who claims only to be hunting one of its kind who is possessing one of them. They discover it is in Chiana, but even when her rider is destroyed, nearly killing her in the process, the creature in Pilot refuses to leave, enjoying the sensation too much. They trick it into being destroyed in a starburst. Meanwhile, Scorpius is desperately trying to investigate wormholes, with surprising resistance from Crichton-in-a-chip.
Talyn has landed on a jungle planet to recover. But the Peacekeeper crew led by Aerin's mother finds them. After lots of running around and fighting, eventually Aerin realises her mother must die, else she will continue to hunt them down. Crichton leads Aerin away while Crais is left to do the deed. We hear a shot...
Desperate to decode the last of the wormhole technology, Scorpius implants the chip in his own brain, and tries to convince the internal Crichton to help, by showing him his abusive upbringing by the Skarrans, and painting the Peacekeepers as the good guys. Virtual Crichton will have none of it, though. Meanwhile, back on Moya, while still searching for wormholes, the crew discover a scientist who has run to them from Scorpius, through a wormhole. The journey eventually kills her, but Crichton realises Scorpius could find them the same way.
Talyn gets too close to a siren star, and starts leaking gas which makes everyone more susceptible to their urges. Stark links to Talyn to help send a dead woman to the other side. Rygel overeats. Crais gets all Captainy. And Aeryn and Crichton can barely keep their hands off each other.
Pilot is fed up with Crichton and D'Argo' constant bickering, and sends the crew off to a pleasure planet for a week. But two days later, Crichton is back, with a fantastic tale of drug dealing, hammer-headed remote eyed aliens, and desperate rescues. [Hilarious!]
Jack, the ancient alien who originally gave Crichton the wormhole secrets turns up on Talyn, accusing John of selling the technology to a war-like race. Crichton denies everything, omitting to mention Scorpius, and suggests that the female he sold his shuttle data to might be to blame. So they go back to her planet, and find it under attack by ancient enemies of the Hynerians, who have teamed up with the Scarrans. Jack says their only hope is to release the data from John's head to build a bomb, so he has to reveal the truth about Scorpius and the neural-chip. Jack tries to remove Scorpius, but in the end, it appears that only Scorpius is left in John's head, and that Aeryn will have to kill him...
...the Scorpius personality dies, leaving John free at last. He helps Jack build the bomb, but they are double crossed, and Jack is killed. In a desperate struggle, John manages to use the bomb to destroy the Scarrans, but gets a lethal dose of radiation.
In a fit of anger, D'Argo hits Chricton, who ends up in a coma. D'Argo's ship is about to self destruct, and the crew need to stop it before it kills Moya. Meanwhile, in his head, Crichton fights a cartoon battle with Scorpius. [Utterly brilliant!]
A distraught Aeryn, desperately mourning Crichton, falls into a trap laid by her mother (not killed by Crais after all) on a planet where they claim they can raise the dead. Eventually everyone is extricated, off to find Moya, Aeryn returned to her old hard Peacekeeper self. Stark stays behind, because he can almost hear Zhaan, but sends his face mask off with Aeryn to give to Crichton.
A group of escaped prisoners, including a female Hynerian and a Scarran, have sought refuge on Moya when the crew of Talyn finally return. Rygel is in love, but Aeryn finds meeting the "other" Crichton very hard. One of the prisoners is a traitor, signalling the Peacekeepers. It's Rygel's new love, and Rygel nearly gets taken as a prize offering, before the others rescue him. Stark's face mask hold a message from John, telling his double that Scorpius now has a lot of highly dangerous wormhole technology. The remaining Crichton determines to find Scorpius and stop him.
D'Argo and Rygel go to negotiate with Scorpius, telling him that Crichton wants to give him wormhole technology, because other wise the Scarrans will get it first. But they end up getting caught up in an inept robbery. Meanwhile, Talyn, accidentally destroys a medic ship, then attacks Moya. The rest of the crew have to convince Moya to let them "switch off" Talyn.
Crichton is on board Scorpius' command carrier. He's finding it difficult to come up with a workable plan to destroy the wormhole data. The Peacekeepers don't like Moya's crew. A senior Peacekeeper officer arrives, and takes the crew captive. Scorpius overrides her. Crichton begins to realise how dangerous the Scarrans would be with wormhole technology. Scorpius accuses Crichton of stalling, and threatens to destroy Earth if he continues.
Crichton decides the only way to stop Scorpius is to blow up the entire Command Carrier. While they are searching for a way to do this, Crais betrays their plan to Scorpius, and the crew are locked up. But it's only a ruse, and Crais' plan is to get Talyn to Starburst in dock, killing them both, and imploding the ship. The rest escape back to Moya, but are talking of splitting up.
Moya and the crew want to bury his remains in the sacred leviathan burial grounds, which unfortunately is guarded by a rogue mad leviathan, who attacks them. So they band together and kill it. Then they all split up and go off in their own directions. Aeryn goes off without John. He flies about, brooding, in his spaceship, and is just about to return to Moya when he discovers Aeryn is pregnant. Just then, Moya gets sucked into a wormhole, leaving John stranded in deep space ... To Be Continued ...