Aeryn saves Crichton and D'Argo, but only by making a deal with Crais. Zhaan has decided to meditate her way to the next level. There's lots of to-ing and fro-ing, lots of deals and double-crosses. But in the end, Talyn offers Crais a direct neural interface, and the two of them starburst away, leaving the rest of the crew on Moya, who also starburts, away from Scorpius.
D'Argo is honoured to be asked to help an aged Luxan holy woman in her death rituals. However, as she is about to die, she detects great strength in D'Argo, draws on it, and is revitalised. D'Argo is overjoyed, and begins a passionate affair with her. However, the strength she drew on was not D'Argo's, but Moya's, and now Moya is dying. They desperately try to save her, but in the end there is only one answer -- D'Argo's new love must die after all.
Chiana is depressed when she discovers her brother has died, so goes down to a planet and joins a group of youngsters who are preoccupied with a ritual leap into a deep chasm. Many survive, but some die. Crichton and Aeryn go down to bring her back, but she doesn't want to leave her new friends. Crichton wants to force her, to save her life, but Aeryn says she must work things out herself. Eventually she leaps -- and survives.
A strange blind alien boards Moya to help the crew build a device to screen them from Scorpius. First he has to take them past some pulsars -- he warns them that their light affects only "lesser species". But they soon all start acting strangely hostile -- even when the pulsars are past. Meanwhile the alien is busily reconfiguring Moya to give him light. Crichton works out there is a problem, that the alien is causing the madness to distract them from what's going on -- he's less affected because of his inferior human vision -- and gets the others to help him defeat the alien. But the hurtful things they said and did to each other during the madness linger on. Crichton, smearing a protective paste on his face: "this smells like puke". Zhaan: "I did pre-digest it."
The crew find old datacam recording, showing the cold-blooded killing of Moya's previous Pilot by Peacekeepers -- and one of them is Aeryn. The crew are horrified, but agree to keep the news from Pilot. But Rygel sneaks the recording to him; he is incensed, nearly kills Aeryn, then rips out his connections to Moya, saying they will stay dead in space until Aeryn leaves. In a series of flashbacks we see the whole plot -- the old pilot would not agree to Crise's demands, and so was killed to allow the new Pilot to be installed. But the technician in charge of the installation, also Aeryn's lover, sabotaged the plot to allow Moya to become pregnant. Aeryn betrayed him, in order to be reassigned to prowler patrol. Current-day Aeryn is distraught at her past behaviour (and she had not realised it had been Moya), and offers to let Pilot kill her, if he will just reattach to Moya to save the others. But Pilot has a secret of his own -- he agreed to be bound to Moya in defiance of his elders, because he was desperate to see the stars -- and so feels responsible for the death of the previous pilot. Eventually he and Aeryn are reconciled, and he is reattached to Moya, with naturally grown connections, that do not cause him constant pain.
An art dealer gives Chiana a picture that appears to predict the future: her lost necklace, her broken leg, her death in a fire. Despite the crew's desperate attempts to burn it, break it, and ditch it, it keeps coming back. Then D'Argo gets speared through the chest -- just as the picture said. It is a trap set for Zhaan by the evil fear-sucking magician who is annoyed with the way she had previously dispersed him. The crew apparently being killed are actually just being sucked into the picture, to frighten Zhaan before she dies. Finally Zhaan manages to defeat him again ... just.
The crew has run out of food, and is starving. Zhaan is the worst affected, and begins emitting spores that are causing allergies and affecting Moya's systems. They come across a gargantuan space monster corpse, being mined for crystals by various aliens, from which a thieving Chiana once fled, and attempt to trade for food. But the only food to be had has to be bought by work in the crystal mines -- which are closed because of a monster. Rygel attempts gambling, but is out-cheated. Back on Moya, Aeryn is having trouble controlling an increasingly paranoid Zhaan. Crichton discovers the mine owner is using the monster to close the mines so he can steal all the crystal. Crichton defeats the monster, gets the food, and feeds Zhaan just in time.
Zhaan and Crichton are stranded in their broken-down flyer, waiting to be picked up by Moya. Zhaan is having nightmares, and Crichton gets her to talk about them. They stem from when Aeryn, Crichton and D'Argo were missing [at the beginning of the season], and Zhaan thought they must all be dead. She, Rygel and Chiana were searching for them down on a planet full of lawyers, when Zhaan was set up for a murder rap. Rygel and Chiana have to defend her and find out who really did the murder, knowing that if they fail, they too will suffer their client's death penalty. Rygel : "This will involve deceit and trickery." Chiana: "At last, we're playing to our strengths."
A badly damaged ship is threatening to attack Moya. Zhaan goes aboard to convince them the crew offers no threat, but the two surviving aliens claim they were attacked by Talon, imprison Zhaan, and fire on Moya. The shield disperses most of the energy, but as a strange side effect, swaps the crew around: Crichton finds himself in Aeryn's body, Aeryn in Rygel's, Rygel in Crichton's, and Pilot in Chiana, Chiana in D'Argo, and D'Argo in Pilot. Now the crew must convince the aliens of their friendliness, and get their bodies back. But the aliens are lying, they originally fired first, and Talon fired back in self defence. Once the aliens are convinced Moya is unarmed, they disable the shield, and prepare to fire again. The crew get the shield partially restored, and the same side-effect swaps them around again. Now Crichton is in Rygel, Rygel in Aeryn, Aeryn in Crichton, and Pilot in D'Argo, D'Argo in Chiana, and Chiana in Pilot. Back on the aliens' ship, Zhaan manages to escape, and disable the aliens. She prepares to return to Moya, but the crew just manage to convince her to fire yet again, and the third burst puts them back in their correct bodies. [An excellent episode, with great acting of each other's characteristics, and very funny in places.]
Moya and crew find a Peacekeeper "lost colony", now very anti-Peacekeeper. They are having a coronation, and the crew, except Zhaan, go down to join in. The Princess has to find someone with compatible DNA before she can succeed -- but her DNA has been poisoned (by her brother, who wants the throne himself), so no Sebacean is compatible. But John Crichton isn't Sebacean.... Meanwhile, Scorpius has arrived. Moya starbursts away, hoping to lure him into following, but he doesn't. Instead, he goes down to the planet, and attempts to get hold of Crichton. The current Empress gives Crichton a choice: marry her daughter, or be given to Scorpius. Aeryn is against the marriage, but the others reckon it is the best choice -- despite the fact he will be a "statue" for the next 80 years. But it looks like things won't get that far, as the Princess's brother attempts to assassinate Crichton.
The Prince's fiancee, actually an undercover agent, saves Crichton's life, and assumes he too is a Sebacean agent, there to stop the Prince becoming Emperor. Crichton beats up the Prince, but no-one else will believe what happened. Then a gas attack nearly kills both Crichton and the Princess -- they are saved by the lizard-servant. On board Moya, one of the Builders is upset she can give birth to a gunship, and orders her to shut down. She complies, much to Zhaan's distress and anger. Crichton agrees to secretly go aboard a freighter to hide -- but it is a trap by Scorpius -- the servant is in his pay. However, once Crichton realises he is unique and priceless, he realises the guard cannot kill him, and escapes (through vacuum!) Aeryn is pleased to see there is still fight in Crichton, but dismayed when he refuses to fight any more, and dashes off. Moya is completely shut down, and Pilot is dying. Crichton marries the Princess, and they both turn to "statues".
Crichton's statue head is stolen, and bounces around between various parties. Eventually it is reattached, and he is restored, by the Sebacean agent. Aeryn's rock-climbing party goes wrong when her companion panics, and they fall. Zhaan discovers that the Builder who killed Moya was doing so to test Zhaan, to test if she would guide Moya responsibly, and Moya and Pilot recover. The injured Aeryn has to drag her worse-injured partner back to civilisation. Crichton, initially elated at being free, discovered the princess is pregnant with his child, and demands to be turned back into a statue. But, because he is not Sebacean, he would not survive a second transformation. So the minister is frozen in his stead. The crew return to Moya. Aeryn gets Crichton to take the compatibility test.
An alien invader catches Crichton in a green sphere, which ejects three versions of him: cave-man, current, and future lizard-like. The sphere, which is sucking Moya into a transdimensional void, demands one of them back as a scientific sample before it will leave -- but which one? Chiana lets the cave-man free -- current-Crichton finds him but refuses to sacrifice him. Future-Crichton says it is the only logical thing to do -- but current-Crichton proposes to sacrifice himself. But then past-Crichton knocks out future-Crichton and carries him into the sphere. Current-Crichton is distressed that his past form, rather than his future form, did the right thing.
The crew have just bargained from food, but there is a suspicion it may contain a parasite, so Chiana and D'Argo get a small, cute-looking Volk to hunt it down. Crichton is having hallucinations about Scorpius. Then D'Argo is attacked by a large monster, and his unconscious body is found full of toxin, which is slowly killing him. The Volk falls under suspicion, especially when the monster emerges from its mouth. But after being pumped full of translator microbes, it manages to communicate with Pilot, and convinces Crichton and Aeryn to let it hunt. Aeryn is still suspicious, and then it attacks Rygel. Crichton and Aeryn hunt it down, and it leads them into a cargo bay. Aeryn shoots it, but then they discover it was leading them to a cocoon, with the real Rygel inside. The other Rygel is actually the parasite. They manage to kill the parasite, but the Volk dies too, in Aeryn's arms.
Crichton wakes up back on Earth, and is told that he crashed Farscape . But he's too wise to fall for that again, tries to strangle his "father", and is restrained. Aeryn turns up as a doctor, and he eventually convinces her to release him. But then it gets weirder: Zhaan, still blue, turns up as a shrink, D'Argo as a hot-shot pilot, Scorpius as a rock drummer, and then Rygel as head of the Space Association. Crichton crashes a car into a truck, but just wakes up back in hospital. Then he throws Rygel off a building, and Crais as a police officer tries to fine him 4 dollars for the crime, but Rygel turns up unharmed anyway. Scenes grow more and more fragmented, then Scorpius turns up for real, saying this is actually an interrogation by the evil creature from the royal planet. He, Scorpius, is being generated by a chip in Crichton's head. Eventually Scorpius "kills" Crichton, allowing the interrogation to pause, and Chricton to kill the interrogator. Crichton then has his memory of the chip erased.
Aeryn returns from a day-long scouting mission in a strange amber cloud -- but she is an old woman. She fights to return to the planet, and Crichton follows. He too gets trapped, and ages. Actually Moya is trapped in a region where time runs very slowly -- it's the rest of the crew who are not aging. They realise the universe outside has passed them by -- everyone they knew is dead. Crichton and Aeryn return to Moya, he an old man, she so old she dies on the trip. Zhaan and Stark (the glowing headed man who shared Crichton's captivity by Scorpius) meld, and work out how to get out of the cloud -- Moya's rear is right at the edge of the cloud, so she must Starburst in reverse. She does, and everything returns to the time as it was before -- only Zhaan and Stark remember what happened.
Crais asks the crew for help in downgrading a too-aggressive Talon's weaponry. While they discuss the idea, a trade ship is destroyed. A sister ship captures Crichton, Aeryn, Zhaan, D'Argo and Stark, and puts them on trial for the incident. We see five different accounts of what happened. Eventually, Stark confesses to the crime, to save the others, and is discorporated (there is a suggestio he may be able to survive this, because of his glow). Then the others discover it was actually Talon who fired.
Two Nebari arrive to take Chiana home. They use drugs to brain-cleanse all of the crew, except Pilot who cannot be cleansed, so is controlled by a collar, and Crichton, whose Scorpius implant makes him able to resist. Rygel also throws off his conditioning early, because of his fast metabolism and three stomachs. Chiana learns her brother is still alive, leading a resistance movement, and one of the two Nebari is his agent. The Nebari had let Chiana and her brother escape, after infecting them with a dormant plague, spread by "sexual congress", and set to be triggered across the galaxy. The double agent refuses to help Chiana, because that would blow his cover. Crichton and Pilot try to fool the Nebari that they are under attack by Peacekeepers, but the lead Nebari merely starts to torture Chiana to death so she won't be taken by them. Crichton calls off the attack, but then the double agent kills his leader, disgusted by her cruelty. Rygel locks up the rest of the crew until their cleansing wears off.
Zhaan is searching for Stark, but D'Argo wants to rescue his son. Just as they are about to come to blows, they find Stark, who had managed to reconstitute himself. He says D'Argo's son is to be sold at a slave auction, and they need money to buy him. D'Argo forces the others to go along with a planned heist by getting himself captured. They rescue him, and Rygel is hidden in the vault, ready to steal some beryllium ingots. Then Scorpius appears -- it turns out it is his ingots being stolen. Crichton overcomes his implant long enough to (maybe) kill Scorpius, and they all escape, with the loot. But the loot has been booby-trapped with some sort of spider-creature...
The crew get to the slave auction too late: Scorpius [not dead, of course] has bought the lot containing D'Argo's son. So they decide to use the loot to hire mercenaries -- Crichton, Aeryn and Rygel go hunting the disparate bunch [all familiar from earlier episodes]. But the loot has turned into Spiders, eating Moya. Zhaan works out the only way to kill them is to burn them -- but that badly injures Moya. The rest return to the injured Moya with mercenaries they can't pay. Suddenly D'Argo's son appears -- Scorpius has let him go, because Crichton has given himself up.
The crew and the mercenaries plan to rescue Crichton, and steal some more loot. There's lots of frenetic activity and running around, but eventually they succeed, with the help of Crais and Taylon.
The crew take Moya and Crichton to a brilliant surgeon for treatment. While Moya is being treated, Crichton, now almost totally under control of the Scorpius chip, escapes, takes his shuttle, and speeds off, sending a signal to the real Scorpius. Aeryn goes after him, but Crichton/Scorpius knocks her out of the sky, and she falls into a frozen lake, and drowns. The surgeon starts operating on Crichton, and removes the chip, damaging his speech centres. Then Scorpius arrives, takes the chip, and "condemns" Crichton to live with his desire for revenge. The season finishes with Crichton lying strapped on an operating table, the top of his skull removed. To Be Continued ...