Astronaut John Crichton's experimental Farscape module is swallowed by a wormhole and spat out on the other side of the universe - in the middle of a pitched space battle. Taken on board Moya - a huge bio-mechanoid "living ship" desperately trying to escape captivity - Crichton is confronted by alien life forms: Ka D'Argo, the fierce Luxan warrior; Rygel XVI, the sluglike Dominar of the Hynerian Empire; Pa'u Zotoh Zhaan, the serene blue Delvian priestess; Pilot, a four-armed creature physically and neurally bonded to Moya, and Oficer Aeryn Sun, an enemy Peacekeeper. In order to repair Moya, Zhaan, D'Argo and Rygel are forced to a Commerce Planet. Pursued by the ruthless Captain Crais, Crichton must use his primitive earth science to devise a means for Moya to slingshot out of range of Crais' ship and into the Uncharted Territories.
Unable to shut off an internal alarm within Moya that is emitting a Peacekeeper tracking signal into space, Pilot makes the desperate decision to crash land Moya on a planet. Once on the planet the crew discover the alarm is deeply embedded in Moya's neural system and they will need to operate to get it out. While searching for a pain-killing agent for Moya's operation, Crichton meets some of the planet's inhabitants - beings who have never before encountered extra-terrestrials. The surgery on Moya is hindered when local military capture D'Argo, and Crichton is forced to choose between Moya's safety and D'Argo's life.
The source of a mysterious rise in Moya's temperature turns out to be an infestation of Draks, a race of intelligent insectoid creatures. Aeryn quickly succumbs to Sebacean heat delirium, a potentially fatal illness, forcing Crichton to bargain with the Draks, who agree to lower Moya's temperature in return for inhabitation of Moya until their breeding cycle is complete. However, this uneasy truce is shattered when lethal Peacekeeper Commandos under the command of Captain Bialar Crais raid the Leviathan.
Rygel borrows a valuable crystal essential to Moya's survival, hoping to impress Tavlek Traders interested in business. However, the Tavleks' real business is holding important hostages for ransom, and they kidnap Rygel and the crystal. Crichton and the others obtain a powerful gauntlet weapon from a captured Tavlek to aid their rescue of Rygel, but they find that using the Tavleks' weaponry is almost as deadly as the Tavleks themselves.
While evacuating survivors of a disintegrating Space Cruiser, Crichton is exposed to a mysterious force field that causes him to jolt randomly back and forth through time and see possible futures. One of the survivors, the seductive Matala, entrances D'Argo, but harbours a more insidious purpose. As Crichton uncovers Matala's plan, his visions of the future become more and more disastrous; no matter what he does, he repeatedly perceives his actions resulting in Moya's destruction.
The crew follows D'Argo down to the city of the Sykarans, and is made welcome by the monarch Volmae. D'Argo, along with the general populace, has become a slave to the addictive, mind-altering tannot root. The artificially euphoric people work endlessly for the powerful Volmae, their minds clouded by the tannot. In his efforts to free D'Argo, Crichton encounters the Sykaran resistance movement who force him to let a large live worm eat its way into his belly as protection against the tannot. In order to free them all from the planet, Crichton realises that he must break Volmae's hold over her people.
Aboard a derelict Peacekeeper Command Carrier, the crew discovers a young female Tech, Gilina. Crichton is immediately attracted, and Aeryn finds herself fighting unfamiliar feelings of jealousy. Rygel is also uncomfortable, forced to confront his convict past. When a gang of fire-breathing Sheyang scavengers arrive and commence hostilities, Zhaan helps D'Argo play diplomat, a role that goes against his Luxan training, but one he must play to keep them all alive.
Crichton is transported into the supernatural realm of the evil Sorcerer Maldis, where he is faced with his arch-nemesis, Crais. Though their confrontation is fierce, they are merely pawns in Maldis' realm. Finding Crichton's body apparently dead, Aeryn and D'Argo try vainly to storm Maldis' fortress. Zhaan attempts a rescue on a spiritual plane, but to do so she is required to invoke the deepest, darkest part of herself, a part she had hoped never to reveal.
An alien geneticist, Namtar, uses the DNA of each crewmember to determine the correct route to their respective homeworlds. Aeryn and Crichton are both disappointed; locating Earth is beyond Namtar's abilities, and Aeryn knows her way home but can never go back. It then transpires that Namtar has a hidden agenda. He injects Aeryn with Pilot's DNA, and she starts to mutate into Pilot! While Crichton desperately works out a way to reverse the process, his efforts are hindered by D'Argo, Rygel and Zhaan, who fight to be the first to go home.
After an accident on Moya, D'Argo starts treating the crew as if they are figures from his past. Simultaneously, Moya takes control out of Pilot's hands and aggressively attempts to expunge all onboard! To work out exactly what triggered these events, Crichton, Aeryn, Zhaan and Rygel have to keep up the charade as D'Argo's past acquaintances, and in the process uncover the Luxan's troubled, phenomenal history. The crew is to discover also that somewhere inside Moya, an amazing change is taking place.
After a close encounter with an unstable wormhole, Crichton and Aeryn take the Farscape Module down to the desert-locked Dam-Ba-Da Depot for repairs. They leave it in the hands of the money-grubbing mechanic Furlow. However, two wolf-like Blood Trackers, Rorf and Rorg, are hunting the crew, and when they capture D'Argo, Crichton actually takes part in torturing the Luxan to maintain anonymity. Meanwhile, Aeryn considers a secret offer from Crais: a tempting proposition to sell out the crew in exchange for her old Peacekeeper life back.
A false distress signal brings Moya to the home of a young Delvian Priestess, Tahleen, who sent out the signal in order to summon Zhaan. While the crew is made welcome, Zhaan is puzzled by Tahleen's motivations; it seems the young but powerful Delvian wants to join in 'Unity' with Zhaan in order to curb her dark side. In the process, Zhaan is forced to confront her own insidious past, and when the Unity goes horribly wrong, Crichton must come to Zhaan's aid, and risk his very sanity to save her.
Whilst flying a Transport Pod, Crichton and Aeryn become ensnared in 'The Flax', an immobilising net-like weapon under the control of ruthless Zenetan Pirates. An eccentric ex-pirate, Staanz, comes to Moya's aid before she too is captured, but he is being pursued by the dangerous hunter Kcrackic. After D'Argo abandons them to search a nearby Luxan vessel caught in The Flax, Crichton and Aeryn are faced with a serious problem: they must depressurize the Pod to make repairs, but they have only one space suit - meaning one of them must die.
After apparent abandonment by Moya, Crichton retreats to an Eden-like planet and ekes out a simple existence in a community of humanoid aliens. He becomes attached to a native girl, Lishala, but others have designs on Lishala that endanger Crichton's life. When D'Argo and Rygel come to the rescue unexpectedly, the locals treat Rygel as a God, but even this apparent blessing has dire consequences for the trio.
Moya's crew encounters an old enemy, Peacekeeper Captain Selto Durka, who is now the brainwashed slave of a mysterious species, the Nebari. Durka and his new Nebari master Salis are returning Chiana, a Nebari criminal, to her homeworld to be 'mind-cleansed'. When Rygel attempts to kill Durka, the Captain's evil personality returns, and he immediately tries to wrest control of Moya from the crew. To save Moya, Crichton desperately needs Chiana's assistance, but she may be better off if Durka succeeds.
Crichton shoots through a wormhole to Earth and finds himself back home, seven months after he left. The original wormhole, it seems, has been open the whole time, and Earth has been fearfully waiting for aliens to invade via the yawning portal. Crichton, though reunited with his father, Jack, is treated with suspicion, but when D'Argo, Aeryn and Rygel arrive in a Transport Pod, he is forgotten in the storm of xenophobia. Though the imminent danger brings Aeryn and Crichton closer than they have ever been, Crichton discovers that his father is not what he seems...
After a botched Starburst, Moya becomes stuck in a dimensional schism; divided into different planes of existence, with the crew scattered and lost throughout these planes. Crichton is witness to various strange phenomena as he explores the fabulously changed Moya. A decision is made to reverse Moya out of the schism, but as this plan gets underway, an alien source warns that their carefully thought out plan will lead to Moya's destruction.
When Moya is forced to dock with an approaching Peacekeeper vessel, Aeryn and Crichton masquerade as Peace-keepers guarding the rest of the crew. The PK soldiers bring on board a mysterious crate; within is contained an intelligent virus, which accidentally infects Chiana. The virus is exceedingly deadly, taking over the minds of its victims. The two crews form an uneasy alliance in order to track down the virus, but it is nearly impossible to tell who will be infected next...
In order to secure a vital tissue graft to save Aeryn's life, Crichton and Chiana disguise themselves as Peacekeepers and infiltrate a secret PK base there. They meet up with Gilina, the Peacekeeper Tech who Crichton met on the Zelbinion. Gilina is able to help Crichton obtain the graft, but before he can get it to Aeryn, Scorpius - a Sebacean/Scarran hybrid - exposes Crichton's charade and subjects him to the Aurora Chair: a torture device used to extract memories from its victims. Scorpius discovers a memory implanted in Crichton's head by the Ancients that Crichton himself was not aware of: information about creating wormholes. To access this hidden knowledge, Scorpius is willing to destroy Crichton's mind.
Determined to rescue Crichton, Aeryn infiltrates the secret Peacekeeper base where Crichton has been imprisoned. Between grueling torture sessions in the Aurora Chair, Crichton is locked in a cell with Stark, a Banik slave who is being subjected to the same torture. Eventually Gilina comes up with an ingenious plan to break Crichton and Stark out of their cell. Meanwhile, back on Moya, Chiana and Rygel contend with the difficult birth of Moya's child.
Still on the run from Crais, Moya responds to a distress call and lands on a highly vegetated asteroid. The crew saves a helpless alien, M'Lee, from a formidable monster, Br'Nee, and in the struggle their transportation is disabled. Stranded for the moment, the crew discovers that Br'Nee was in fact part of a research team that was annihilated by the 'bone eater' M'Lee. When Zhaan then disappears, it seems there are even darker truths to be revealed.
When Rygel offers Moya's crew to Scorpius in exchange for his own freedom, it falls to D'Argo and Crichton to engineer a diversion that will allow Moya to escape. On board the Command Carrier, Rygel is witness to Scorpius supplanting Crais as Commander, and also to Crais' own crisis of faith. Crichton sees only one way for Moya to escape: he and D'Argo must carry out a spectacular suicide mission to stop Scorpius in his tracks.
