Chricton found an ancient leviathan and pilot, come to the sacred burial ground to die, and has been trying to develop the wormhole equations. Sikozu, a new alien, arrives, destroying his work, closely followed by a bunch of "Klingons" who want to harvest the dying leviathan. Rygel and Chiana turn up, having been through some harrowing times. Chricton decides to stop dreaming of Aerin and the baby.
Most of the team meet up in the middle of an archeological dig looking for powerful artefacts, and are then captured by Peackeepers. Crichton suffers Granny's visionary dust, which leaves him knowing too much, and he is forced to reveal it to this season's new "mad military commander"
People escape, are recaptured, and escape again, a lot. Scorpius is killed [but I bet he doesn't stay dead]. The gang eventually con the Peacekeeprs, rescue the dangerous artefacts, and restore the planet. Jool stays behind.
The crew, short of food, land on a volcano planet, and stumble across a bunch of hijackers, who are very unhappy to see them. Eventually they escape, with the help of D'Argo's vomit, and with a nice new "belt shield". They make contact with Moya.
Back on Moya Crichton discovers a dreadfully sick Aeryn, and Scorpius, claiming to have saved her life, asking for asylum. (Crichton does notice the pattern here...). Then a giant ship arrives, accusing Aeryn of assassination, and claiming to have made her sick. The crew have to get the antidote and leave before the Peacekeepers launch a deadly missile at Moya. But Aeryn refuses to cooperate.
A giant space plant infiltrates Moya, and starts killing her. While fighting the plant, Aeryn tells Chaina she doesn't know who the father of her baby is -- due to some implausible Peacekeeper physiology, it could be from before she even joined the crew. This news gets back to Crichton. The plant is defeated, with help from Scorpius. D'Argo is elected captain.
Crichton and Chiana get trapped in a game world, run by an avatar of Stark. They have to escape to help the crew of Moya recapture an escaped Scorpius. But when they do, something still seems rather strange. [At least here, something plausible happens if you die in the game: it merely resets to the beginning of the level. And there's a nice riff on Max Headroom , and a nod to the HHGTTG elevators.]
Bounty hunters have captured Moya's crew, but Pilot cleverly manages to warn a returning Crichton, who then has to rescue them all. But to make life more difficult, the bad guys have shrunk the crew to a few inches high. [There is a nice scene where Sikozu runs through the standard reasons why this is of course impossible, and Chiana tells her that it's happened anyway.] An escaped Scorpius tells Crichton the head bad guy is a Skarran in disguise. Crichton, with help from Scorpius, saves the day.
Aeryn is subliminally coerced into murdering a clan leader, bringing his world on the brink of war. Crichton has to find the real killer while Aeryn is pursued for the crime, while they are being coerced to kill each other.
The crew suffer strange symptoms after eating alien clams, and discover they have been poisoned. A doctor is blackmailing them for the cure, but then his supply of antidote is cut off by a group of women planning a coup. Aeryn and Sikozu attempt to deal with them, but are taken hostage. Crichton and Rygel go in after them, in drag. Scorpius manages to stave off their symptoms long enough for them to escape.
Crichton is sucked into a wormhole and interrogated by one of its inhabitants. He is shown various bizarre "unrealised realities" that his wormhole exploits may result in. He is finally released, and told how to get back to Moya. But he reappears in Earth orbit...
Crichton and the crew find themselves on Earth, a few days before the Challenger shuttle launch, with Crichton's father planned to fly on it. Crichton must change that, without disrupting everything else, otherwise his future will not happen. Back on Moya, the Peacekeepers arrive, searching for Crichton, and leave a little surprise behind for him. Having restored the timeline, the crew returns to Moya back in the present, and Crichton's father is waiting for him...
First Contact between Earth and the crew of Moya, but the government suits want all the technology for the US, and Crichton doesn't agree. Scorpius is taking precautions to block the wormhole to Earth should the Peacekeepers reappear. Meanwhile, the Peacekeeper creature hunting Crichton is on Earth, causing mayhem. Crichton decides he has to leave. Aeryn discovers he's been taking drugs to forget her.
Chiana acquires a slave, wanting to free her. But she, in the form of a giant spider, sucks the essential strength out of the crew, and they must regain it before they die. Crichton tells Aeryn he's been avoiding her, so that Scorpius won't use her against him to get wormhole information.
Scorpius takes Crichton, D'Argo and Rygel for mental training, ostensibly to help Crichton resist the Scarrans. Another trainee is D'Argo's brother-in-law, who accuses D'Argo of murdering his wife, the crime for which he was imprisoned. Thoughts of Luxan hyper-rage and blackouts cause D'Argo to wonder if he really did.
Grayza meets a Scarran, to arrange a truce. Aeryn and Chiana scupper the deal, but Aeryn and Grayza are captured by the Scarrans.
Crichton watches an intercepted documentary about the "Alien Visitation" to Earth, while the crew hunt for Aeryn. Crichton remember something relevant he learned while escaping from the wormhole.
Captive aboard a Scarran freghter, Aeryn is tortured to reveal the identity of her baby's father. Meanwhile, Scorpius and Crichton travel through the wormhole to the "unrealised reality" Moya, and torture her crew to reveal the location of the Scarran base Katrazi.
The crew rescue Aeryn by causing a plague, but Scorpius is captured. Crichton learns that Scorpius has been bugging his brain, so knows about wormholes, and must be rescued before he tells the Scarrans.
The crew decide they have to rescue Scorpius before he tells the Scarrans about wormholes. They return to Katrazi, where they pretend to be selling Crichton's wormhole knowledge to the highest bidder, all the while fomenting a riot. As insurance, Crichton carries a fission bomb with him, with a dead-man's handle linked to his emotional state. A vengeful Stark is brought in to torture Scorpius. The riot lets Crichton and Aeryn rescue Scorpius, but he double crosses them, pinning John to the ground, as the monitor on the bomb starts ticking...
Scorpius stops the crew escaping, because he wants to destroy a secret flower that is vital to the Scarrans. Crichton learns Scorpius never knew of the wormholes; that was just a fail-safe ploy by Harvey (Crichton's in-brain Scorpius) once he detected Crichton was going to betray Scorpius. Lots of bluff and counter bluff, toing and froing in excavator elevators, and gunfights ensue. Eventually Crichton uses the bomb to destroy the flower, and they all escape.