John Crichton voiceover during opening credits (Season 1 and 2):
- My name is John Crichton, an astronaut. A radiation wave hit and I got shot through a wormhole. Now I'm lost in some distant part of the universe on a ship, a living ship, full of strange alien life forms. Help me. Listen, please. Is anybody out there who can hear me? I'm being hunted ... by an insane military commander. I'm doing everything I can. I'm just looking for a way home.
John Crichton is an IASA astronaut working on the experimental Farscape project. During the Farscape-1 test flight, a wormhole appears, pulling Crichton to a distant part of the universe. He arrives and finds himself in the middle of a space battle, and the Farscape-1 module is immediately clipped by a small craft, which then spins out of control, hits an asteroid, and explodes, killing the pilot. Crichton is then captured and brought aboard a large ship, which turns out to be a living ship of the Leviathan species, named Moya.
On board are Luxan warrior Ka D'Argo, exiled Hynerian Dominar Rygel XVI, and Delvian priestess Pa'u Zotoh Zhaan, three prisoners who have taken control of Moya and are escaping from the regime of the militaristic Peacekeepers. Eventually, the prisoners manage to remove Moya's control collar and starburst away from the battle. Pursuing Peacekeeper Officer Aeryn Sun's Prowler is caught up in the starburst and she is taken aboard soon after Crichton's arrival. Aboard the Peacekeeper ship, it is discovered that the pilot who hit Crichton's ship and was killed was Tauvo Crais, brother of the Peacekeeper captain Bialar Crais, who now vows revenge on the pilot of the "white death pod."
Catching Crichton, Crais declares he will dissect and kill him. Aeryn, however, declares she thinks the collision was an accident. In retaliation, Crais declares her "irreversibly contaminated" due to prolonged contact with an unfamiliar species, which will result in her death. Having nowhere else to go, both she and John join the unlikely band of allies, and they escape from Crais.
Seeking to avenge his brother's death, Crais pursues Moya through the Uncharted Territories. As Moya attempts to evade the Peacekeepers, the renegades start to overcome their initial dislike and distrust of each other and come together as a working crew. During this time, the backgrounds of the three "criminals" on Moya are explored: D'Argo was falsely accused of murdering his Sebacean wife in a bout of Luxan hyper-rage; Rygel, the former ruler of the 600 billion subjects of the Hynerian empire, was deposed by his treacherous cousin Bishan and handed over to the Peacekeepers; and Zhaan killed her lover and mentor after he sold out their home planet to the Peacekeepers. Crichton, meanwhile, seeks a way to return to Earth; Aeryn, now exiled from her own people, must make a new life for herself. During mid-season, their lives are further complicated by the discovery that Moya is pregnant as a result of D'Argo breaking a contraceptive shield installed by the Peacekeeper Leviathan expert Velorek, and by the addition of to their ranks of Chiana, a Nebari female and fugitive from her own people.
Crichton comes into contact with a mysterious race known as the Ancients; they implant the equations and a sort of "sixth-sense" for wormhole travel in his subconscious mind. Oblivious to the existence of this knowledge, Crichton attempts to embrace his new life aboard Moya, but is captured by the Sebacean-Scarran hybrid Scorpius when he tries to sneak onto Scorpius' secret Gammak Base to steal medical supplies to treat Aeryn's otherwise fatal injury caused by Larraq. Scorpius discovers Crichton's receipt of the wormhole knowledge using interrogation with the memory-scanning Aurora Chair, and secretly implants a neurochip inside Crichton's brain to attempt to unlock the knowledge for use in his own wormhole weapons project.
With the assistance of Chiana, Moya gives birth to a prototype leviathan hybrid gunship, which Aeryn names Talyn. The crew help Crichton and fellow prisoner Stark escape from Scorpius' clutches, but are then trapped on Moya, unable to evade the Peacekeepers hunting for them in the asteroid field around the Gammak Base while the infant leviathan is slowing them down. After Rygel attempts to sell the others out to Crais, both the Hynerian and the Peacekeeper captain flee to Moya when Crais' command is usurped by Scorpius. John then formulates a plan to blow up the Gammak Base (which is on a moon covered in oil), have Aeryn in her Prowler rescue them, return to Moya, and starburst to safety while the Peacekeepers are too distracted by the explosion to track them. The plan goes awry when Crais steals Talyn, and Aeryn is unable to get to D'Argo and Crichton due to enemy presence. As the season ends, the Gammak Base explodes spectacularly, but Talyn is missing, Aeryn is menaced by enemy Prowlers, and the free-floating D'Argo has become unconscious from too much time without air.
- Editor's Note: All Commerce Planets will be numbered according to chronological order. Some planet names were fabricated for classification purposes and are labeled with a *.
- Asteroid field
- Botany asteroid
- Commerce Planet 01
- Commerce Planet 02
- Drak Swarm
- Gammak Base
- New Moon of Delvia
- Zelbinion wreckage