Commander John Crichton, IASA astronaut and son of an astronaut, takes his Shuttle Farscape on a solo flight to test his propulsion theory. But something goes wrong, he is sucked into a wormhole, and flung across the galaxy. He is caught up in a battle as escaped prisoners flee the Peacekeepers in Moya , a stolen space ship. His side is chosen for him when he accidentally kills the brother of Peacekeeper Captain Crais.
Rygel attempts to impress the brutal Tavleks, highly volatile due to their gauntlet stimulant drugs, with his bargaining skills. Instead, they kidnap him and hold him to ransom -- not knowing that he has been deposed and his people will not pay for his return. However, Rygel has a vital part of the ship's system on him, so his crewmates are forced to rescue him, whether they want to or not. Zhaan detoxes a Tavlek captive, but he returns to the drug when freed.
During the rescue of two aliens, Matala [Lisa Hensley] and Verell [John Clayton], Crichton is exposed to a mysterious force in their shuttle, giving him flashes of a deadly future. Each time he tries to do something different, the future gets worse -- more people die. Ka D'Argo is acting strangely -- his people are ancient allies of the aliens, and he feels something for Matala. Crichton has to convince him Matala is actually an enemy spy, before they all end up dead.
A Peacekeeper tracking device is activated in Moya. In order to jam the signal while they attempt to deactivate it, the crew land Moya on a planet, in a swamp. Moya, being alive, will find the deactivation process very painful, since the signal generator is wired into her. Crichton, D'Argo and Aeryn go off to look for some ship anaesthetic. Rygel, the only crew member small enough to get to the device, attempts a deactivation while Zhaan shares Moya's pain. Crichton is discovered by a native boy, and his mother, who runs a small government funded alien watch programme from her farm. She is thrilled, but realises the government will only dissect Crichton, so helps him escape. Rygel completes the disconnection, and the three return with enough anaesthetic so that Moya can take off again.
Moya hides from a Peacekeeper scout behind what appears to be a dust cloud. But the dust is actually a swarm of bugs who are about to reproduce. The bugs infect Moya, start producing look-alikes of the crew, and rack up the temperature. Aeryn, whose species cannot tolerate heat, begins to get dangerously ill. Eventually the crew communicate with the Queen bug, through Zhaan, and convinces it they mean no harm, and to put the temperature down. But then the Peacekeeper scout finds them, boards, and starts killing look-alikes. The Queen thinking the crew have reneged, puts the temperature back up. Aeryn starts getting sick again, but so do the boarders. [What? You can defeat these elite Peacekeeper marines just by turning up the thermostat ?!] Crichton convinces the Queen the crew really is on her side, but to keep the temperature up just until the Peacekeeper boarders are incapacitated. One Peacekeeper survives the fight, and is allowed to return, to tell his boss that the whole of Earth is full of people a mean as Crichton. Aeryn survives, just.
Caught in the grip of some strange rage that makes him want to kill Crichton, D'Argo goes down to the planet Sykar. But when the others go down after him to bring him back, they find a strangely bucolic D'Argo who wants to stay there as a farmer, amidst an orange clad docile population living in the midst of a decaying civilisation saturated with Orwellian broadcasts ("Tomorrow is a rest day"). Rygel starts farting flames, so Aeryn, who won't be able to cope with the next day's heat, is assigned to take him back to Moya for diagnosis. She has to solve Rygel's problem using her brain, rather than a gun, for once. Crichton and Zhaan try to persuade D'Argo to come back with them ... but then Crichton is attacked by some rather less docile farmers, who deliberately infect him with a worm, and Zhaan becomes strangely docile, too. The food is drugging the majority of population, but the worm, introduced by one of the immune few, protects Crichton. It turns out the population is being drugged by the Peacekeepers, who are getting them to grow a vegetable that they (and Rygel's innards) convert to deadly weapons. Crichton brings the population out of their daze, and persuades them to resist.
The crew find a disabled warship. Crichton and Aeryn go to investigate, and discover Gilina, a Peacekeeper technician -- the only survivor of a raid by a salvage crew. Aeryn is initially hostile, because she believes Gilina will betray them -- but gradually her attitude softens. And Gilina, initially treating Aeryn as a traitor, also softens. Crichton and Gilina fall for each other. Meanwhile, Rygel is on a voyage of remembering -- because this was the ship where he was first captured and tortured. He cannot overcome his memories until he finds his torturer Durka -- dead and desiccated. Then the scavengers reappear, and D'Argo has to hold them off with bluff, until the tech can repair the battleships screens. "You had nothing. And you used it very well."
An evil magician forces a disembodied Crichton and Crais to fight. Crichton tells Craise that his brother's death was an accident, but Crais doesn't care; he just wants revenge. A local priest convinces Zhaan the only way to beat the magician is to combine forces, and for Zhaan to fight. She is initially reluctant, but eventually agrees. The local dies in the resulting battle, and Zhaan is distressed to find that some of her suppressed barbarism has resurfaced. Crais, back on his ship, ventures deeper into the uncharted territories in search of Crichton.
A famous biologist can tell from a DNA sample where the subject's home world is. He doesn't have Earth on his database, and Aeryn refuses to participate, because she can never go home -- so he offers to tell D'Argo, Zhaan and Rygel where their home worlds are, but only in exchange for one of Pilot's arms. They agree, forcibly take one of Pilot's four arms, and exchange it for a data crystal. They bicker about the order of going home, but then they discover only one of the locations can be read from the crystal, which leads to a really serious falling out. Meanwhile, Aeryn has decided to ask the scientist to find a Sabacean colony world for her. However, instead of taking her DNA, he instead injects some of Pilot's into her, and she starts undergoing a terrible transformation. Crichton discovers from the scientist's "assistant" that the scientist is stealing DNA from all sources to augment himself to perfection -- and that he wants Pilot's rare multitasking ability. He also discovers that the data crystal will wipe Moya's memory if it is ever read. He works with the assistant to stop the scientist (who regresses back to his original form -- a laboratory test animal), saves Aeryn, and destroys the crystal.
During a routine patrol of Moya to check out for Peacekeeper technology, D'Argo stumbles across some kind of plate, which breaks, and expels him outside into vacuum. The others rescue him, but he keeps seeing them as his old family: Zhaan as his wife, Rygel as his son, and Crichton as his brother-in-law. Meanwhile, Moya seems to be closing down life support, and taking over the DRDs -- Pilot is comatose, and Aeryn has to try to run the ship as best she can. Initially the crew suspect a virus has infected Moya when D'Argo broke the plate -- but then they discover the material is the same genetic structure as Moya. Eventually they discover that she is pregnant, and was trying to protect the fetus. They persuade her they are no danger. At the end we discover D'Argo's dead wife was a Sabacean.
Crichton and Aeryn are testing out Farscape when they manage to replicate the conditions that lead to the original wormhole [slingshotting during a solar flare -- oh, well] and an unstable wormhole appears. Crichton wants to try it, but Aeryn convinces him otherwise -- and is a bit peeved that her would take her into the wormhole just like that. The jaunt damages a plasma feed, and Moya won't let them back on board, because of her unborn child. So they go down to the planet to get it fixed. There they discover a broadcast message from Crais, offering a substantial reward for D'Argo, Zhaan and Rygel. Consequently, there are a number of bounty hunters around. Crichton does an alpha male impression to cow two of them into accepting him as leader. Aeryn discovers a message from Crais offering her honorable retirement if she returns. D'Argo goes down to the planet to bring them back, and is captured by the two bounty hunters. Aeryn fights off another bounty hunter, but is blinded by exposure to the light from another flare. Zhaan has a much more interesting reaction to the flares. Crichton and D'Argo escape, and the bounty hunters now realise Crichton is their enemy. They have them pinned down, but Aeryn has reprogammed the message from Crais to say there is no longer a reward -- and so the bounty hunters wander off. Crichton has to pay for his shuttle's repairs with the data about the wormhole. Aeryn's sight gradually returns. She admits she knew the message from Crais was a ploy, but that she just wanted to feel for a while as if she could return.
Aeryn is teaching Crichton how to pilot an attack craft -- he's a very slow learner -- when they get caught in an invisible web. Moya gets a visit from an ex-Zenetan pirate, who warns the crew about the Flax -- a trap laid by the pirates to capture spacecraft. The crew try to warn Aeryn and Crichton, but too late, they are all ready trapped. So the ex-pirate and D'Argo go off in a spacecraft straight out of a steam punk nightmeare (it has a furnace that needs to be stoked!), ostensibly to rescue them, but first to stop off at a ship that has maps of how to find his home world. Meanwhile, Aeryn and Crichton are in desperate straits -- there is an oxygen leak that can be repaired only by venting the atmosphere -- but Crichton's helmet is broken. He has to teach Aeryn how to weld, and how to do CPR so that she can resuscitate him once she's finished the repair. Back on Moya, two real Zenetan pirates turn up, looking for their ex colleague. Fortunately, they are not interested in Moya -- they've had bad experiences with pregnant Leviathans before. Rygel plays one at a board game for high stakes -- and loses. He's forced to give up D'Argo's co-ordinates. The pirates speed off, and Rygel informs a horrified Zhaan that he lied. Aeryn has been unable to complete the welding in time, but has just managed to resuscitate Crichton. They realise they are both about to die, so engage in a desperate pre-death clinch. At this point D'Argo turns up, to his amusement and their embarrassment, having decided to rescue them rather than search for his maps.
Moya and the crew run across a Delvian sect, who are planning how to retake their planet from the Peacekeepers. But the madness is coming upon them, and they need to regain control. Zhaan agrees to help, by melding with the sect leader so that she can learn about Zhaan's priestly control, which took her decades to learn. But the sect leader, wanting to learn quickly, steals her powers, leaving her subject to madness if her now-uncontrolled anger breaks free. The Delvians play with the minds of the rest of the crew, to stop them helping Zhaan, but some of them are upset by what their leader has done. One of them, who is pretending to be Crichton's (non-existant) wife, frees him from the mind-games, and he melds with Zhaan to restore (some of) her equilibrium.
Crichton storms off in Farscape to get some time alone, but is horrified to then see Moya starburst away. He thinks the others have abandoned him. Luckily, he makes planetfall, and finds an idyllic pastoral community. Meanwhile, the others are searching for him back along Moya's surprise starburst path. They find him, but the planet has a power-absorbing device that means it will be hard to rescue him. Rygel and d'Argo get stranded with him -- and the community recognises Rygel as a deity come to lead them to the light. They are actually the descendants of people from a planet in Rygel's ancestors' empire, deliberately stranded. They are just about to burn Rygel as a false god when Crichton deduces how to fulfill the prophecy, and free the people. Although they want him to stay, he goes back to Moya to continue his search for home.
Coming out of starburst, Moya accidentally damages another ship, and its complement of three has to be rescued. Unbelievably, one of these is Durka, the Peacekeeper captain who tortured Rygel a hundred cycles ago, and who Rygel thought dead . But he had faked his death and run -- and is now cured of his evil ways. Rygel is unconvinced, and tries unsuccessfully to kill Durka with a home built grenade, nearly killing Crichton in the process. The other rescued aliens are a captor taking his prisoner, Chiana, to be "cured" in the same way as Durka. But Chiana escapes, and Durka's conditioning is broken by Rygel's violence towards him. Durka takes Aeryn and Rygel hostage, and hijacks Moya. Crichton and Chiana team up to capture Durka, but fail. Durka is about to torture Aeryn to persuade the others to restore starburst when Rygel tells him the reason they can't starburst is because Moya is pregnant. So Durka heads off to kill the baby. Crichton manages to build a better grenade than did Rygel, and sends Durka off in a crippled scout ship.
Pilot finds a wormhole, and Earth is visible at the other end! Crichton heads home in Farscape , but when he gets there, everyone seems strangely hostile. Then Aeryn, D'Argo and Rygel arrive to check up on him, because Earth disappeared when he went through the wormhole. Some of the humans freak out, and Rygel ends up vivisected. Then they take D'Argo away. So Crichton and Aeryn go on the run. But eventually Crichton realises all is not what it seems. [The audience has realised this much earlier, if only because we know this is an on-going series.] In fact, an alien race who are looking for a new home are testing him to try to determine Earth's reaction. They say if everyone was like Crichton, it would be fine, but he knows too many people who would be hostile. So it's everyone (including Rygel) back on to Moya -- but at least Crichton and Aeryn got a night of passion for their trouble.
The crew are sitting round, eating, saying they should leave the pregnant Moya, because she can't starburst very often. They don't realise she can hear them through the DRDs. Worried they might desert her, she starbursts early to prove she can -- but she can't. They end up stuck in starburst-space, Moya split into four parallel zones (normal, sickeningly slow red, deafeningly fast blue, and funny yellow), with some of the crew in each. They have to get all four zones working together to blast out into safety again, where they assure Moya they won't leave her.
The crew run across some real Peacekeepers in a damaged ship. Crichton pretends to be a Peacekeeper Captain, Aeryn his Lieutenant, and the rest prisoners. The Peacekeepers urgently need to take a strange capsule to a Peacekeeper base, and commandeer Moya for the purpose. Aeryn and Captain Larraq hit it off. Rygel can't contain his curiosity and opens the capsule -- which contains an intelligent malevolent virus that first takes over a Peacekeeper, then moves into Chiana. The virus works its way through most of the two crews [fortunately for the plot it can inhabit a host only once] until all the Peacekeepers except Larraq are conveniently dead. Larraq takes Aeryn hostage, and stabs her, before escaping in a shuttle, which Chricton blows up.
Aeryn tells everyone she is recovered from her stab wound, but Crichton discovers she will in fact die from it very soon, unless she gets a nerve graft. Crichton takes on the identity of Captain Larraq, and he and Chiana go to the Peacekeeper base, where they meet up with Gilina, the PK Tech . She manages to get the medicine for them, but Crichton is captured. Chiana escapes, and takes the medicine back to cure a nearly-dead Aeryn. Crichton is tortured for information by the Peacekeeprs, including Crais. It appears he knows more about wormholes than he realises, courtesy of his alien testers .
Crichton is resisting the mind probe, not because of the wormhole technology, but because he might give away his relationship with Gilina. But she fixes the machine to insert a false memory -- of Crais plotting with Crichton. So Scorpius' attention turns to Crais, who goes into the chair. He too fights the probe, but eventually Scorpius discovers his hidden memory, again not of wormhole tech, but of killing his second officer and ignoring his recall. Moya gives birth, to a be-weaponed baby Leviathan. Back in Crichton's cell, he discovers his cell mate is not mad, but merely has a glowing head. Then a still-weak Aeryn, accompanied by Zhaan and D'Argo, rescue Crichton and his cell-mate. Gilina is fatally injured in the final fire fight.
Crew, Moya and baby are lost in an asteroid belt, hiding from Crais and Scorpius, when they receive a distress call. They go to the asteroid source of the call, and discover two creatures, one a helpless-looking girl, who tunrs out to be a murderous bone eater, one a hideous looking monster, who turns out to be a botanist being hunted by the girl, but who was in turn responsible for the girl's plight. Meanwhile, Aeryn goes on board the baby Leviathan to try to get it to trust its mother. We discover Zhaan is a highly evolved plant. After several twists about who is really the baddy, the botanist ends up dead when he tries to kidnap Zhaan, and the bone eater manages to control her hunger long enough to let the others escape, having been promised thousands of Peacekeepers to eat.
Moya and crew are still hiding in the asteroid field. Rygel goes to the Peacekeepers and offers to sell out the crew in exchange for his freedom. But the disgraced Crais, in fear of his own life, convinces Rygel that Scorpius means to renege on the deal, so Rygel and Crais return to Moya. If her baby keeps close to her while Moya starbursts, he should be dragged along, so they can both escape. A diversion is needed to draw away the Peacekeepers first. Crichton and D'Argo load a shuttle with explosives, and head off to blow up the Peacekeeper base. Scorpius follows when he realises Crichton is on board -- Scorpius wants the wormhole technology. Just before the shuttle blows, Crichton and D'Argo leap into space, waiting to be saved by Aeryn. But Crais steals the baby leviathan, so Moya refuses to starbursts. Crichton persuades her the only way to save her child is to save herself first. So in an end-of-season cliffhanger we have everyone separated, with D'Argo slowly dying in the vacuum of outer space. To Be Continued ...