Episodes 45 - 66
John Crichton's voiceover during the opening credits changes this season, and consists of two different messages overlapping (the second message falls within the parentheses below):
- "My name is John Crichton (I'm lost), an astronaut, (shot through a wormhole) in some distant part of the universe (I'm trying to stay alive) aboard this ship (this living ship) of escaped prisoners (my friends). If you can hear me, (beware). If I make it back, (will they follow)? If I open a door, (are you ready)? Earth is unprepared (helpless) for the nightmares I've seen. Or should I stay, protect my home, not show them you exist. But then you'll never know … the wonders I've seen."
The appropriately titled season opener tells fans everything they need to know about what is to come in Farscape's third season: Season Of Death. This season sees the first major cast change in the series, with the departure of Virginia Hey early in the season. Paul Goddard, Lani Tupu and Wayne Pygram all saw their characters Stark, Crais and Scorpius become regulars (and get berths in the opening credits); the season also saw the addition of Tammy MacIntosh as Jool (although a regular, MacIntosh was only ever credited as a guest star and in one episode went completely uncredited). The final episodes of the season saw the debuts of two new cast members: Rebecca Riggs as Grayza and Melissa Jaffer as Noranti. By the end of the season, however, both Goddard and Tupu had departed as on-screen regulars, with Crais being killed off (Goddard would return in Season 4, while Tupu would continue providing the voice of Pilot).
The Diagnosan heals Crichton with a tissue graft taken from an Interion, a species which is a compatible donor for humans, but all is not well. The neural clone of Scorpius, Harvey, remains in Crichton's brain, but without the neurochip to strengthen it Crichton is able to re-assert himself as the dominant personality. Zhaan uses her spiritual energies to bring Aeryn back from the edge of death - the former Peacekeeper having been frozen in stasis before being fully dead. This revival leaves Zhaan incredibly weak and dying. Chiana's relationship with D'Argo also turns sour as she panics at the sedentary plans on a farm D'Argo has for their future. She begins a secret affair with his son Jothee. Moya and crew leave the ice planet with two frozen 'donors' in tow, the cousins of Crichton's brain tissue donor. Crichton feels guilt for having benefited from the loss of another's life, and hopes that they are related to humans and might have valuable information, and that their lives can later be saved, as Aeryn's was.
Chiana and Jothee's actions, upon discovery, destroy the relationship between themselves and D'Argo, and Jothee leaves Moya. During this, one of the pods containing the Interions is accidentally opened and the person inside emerges only to quickly die. The crew tries desperately to find a planet with the kind of soil Zhaan needs so she can heal and replenish her energies, but they may be too late: an accident involving a wormhole leaves Moya injuriously fused with another ship. Zhaan sacrifices her own life to free Moya and her crew from the wormhole that would have torn them apart, by piloting the doomed alien vessel and rematerialising it separated from Moya. She returns to her goddess and is at peace.
During the wormhole crisis the female Interion, Joolushko Tunai Fenta Hovalis, known to her friends by her full name, and nicknamed 'Jool' by Crichton, awakens from her frozen stasis and makes her presence felt on Moya. An academic ingenue, kidnapped, and frozen whilst taking a multi-civilisation tour holiday, Jool is disgusted by her new surroundings and the inferiority of her traveling companions, and holds a short-lived grudge against Crichton due to her cousin having been killed to save him. However, she has nowhere else to go so joins the crew.
During an encounter with a dying Leviathan that has been taken over by a mad scientist criminal, Crichton is 'twinned' — split into two completely identical Crichtons, both equal and original to each other. Crais and Talyn reappear, being pursued by a Peacekeeper retrieval squad, which results in the crew having to split up for the safety of the defenseless Moya. Crais, Aeryn, Rygel, Stark and one of the Crichtons escape aboard Talyn, leaving D'Argo, Chiana, Jool and the remaining Crichton aboard Moya.
Missing Aeryn, Moya's Crichton becomes obsessed with the wormhole studies that could get him home. D'Argo, still devastated by Chiana and Jothee's betrayal, finds solace in repairing a strange vessel of Luxan origin (that he later names Lo'La after his late wife). After an encounter with a strange energy rider creature, Chiana is left with extrasensory powers that leave her increasingly disoriented and blinded every time she uses them - she can sense the future, and slow down her perception of the present.
Aboard Talyn, Aeryn and the other Crichton begin a passionate relationship. However the retrieval squad catches up and Aeryn is subjected to a painful reunion with her mother, Xhalax Sun, who commands the Peacekeeper retrieval squad assigned to capture Talyn and Crais. Eventually the crew defeat the squad, and Crais seemingly kills Xhalax. Later, Crichton and the crew fight to keep wormhole technology out of the hands of the Scarrans, with Crichton sacrificing his life to this end. Aeryn is completely devastated and flees Talyn to live a reclusive life on a strange planet of mystics to mourn Crichton and, she hopes, speak with the dead, Xhalax returns, having been spared by Crais in return for her calling off the retrieval squad, looking for revenge however is killed when she falls out of a windon. Stark believes that he hears Zhaan's spirit calling to him and leaves Talyn to find her.
Eventually the crew reunites aboard Moya. The crew's relationships are stressed; Aeryn has retreated into her Peacekeeper training, shutting herself off from emotions. She refuses to look at the other Crichton and will barely speak to him. The crew finds a semblance of unity in a new goal: aiding Crichton in destroying Scorpius' wormhole research, which they fear would otherwise give the Peacekeepers access to the known universe, including Earth, as well as access to vast new destructive powers. Rygel and D'Argo meet with Scorpius on a neutral planet and negotiate a deal to allow Crichton access to Scorpius' lab on his Command Carrier, allegedly so that he can assist in the furthering of wormhole technology, but really so that he can secretly sabotage the project.
Talyn meanwhile becomes increasingly wild and uncontrollable, unable to reconcile the peaceful Leviathan and the aggressive gunship sides of his nature. When he destroys an innocent ship and later attacks Moya, the crew agree to put him into a coma until they can find a way to remove his violent tendencies.
Scorpius grants the crew safe passage aboard his Command Carrier while Crichton continues his research; however Scorpius himself runs into problems when his careful plans are halted by Commandant Grayza, who is seeking to establish a peace treaty with the Scarrans. Realising that they can only destroy the wormhole project by destroying Scorpius' Command Carrier, Crais and the mentally unstable Talyn decide to sacrifice themselves and die warrior's death. Talyn performs a final suicidal starburst inside the Command Carrier to blow up the ship, destroying both the wormhole technology research and Scorpius' career.
After Moya carries Talyn's remains to the sacred Leviathan burial space, the crew splinters, pulled apart by the currents of their differing goals. Aeryn decides to leave Moya and join a group of renegade Peacekeeper assassins. She is too distressed by the complicated prospect of living alongside this surviving Crichton while having experienced a fully realised relationship with the other, deceased Crichton. Crichton tries to prevent her departure, and the two argue fiercely. Eventually, they decide to flip a coin to make the decision for them, as Crichton has said that it is fate that the two of them be together, and Aeryn wants to put that fate to the test. Crichton loses the coin toss, and Aeryn departs along with everyone else (apart from Jool). Crichton mopes in his Farscape module and while there, he thinks over what he has recently learned via a mysterious old woman, Noranti, a former prisoner rescued from the Command Carrier who has stayed on Moya to repay her "debt" to Crichton for saving her. Crichton realizes that his dreams of a quiet existence back on Earth with Aeryn as his wife are untenable. Then, with the intervention of Harvey, he realizes Noranti has left a latent message in his brain: Aeryn is pregnant. He has lost his home, he has lost his friends, and now he has lost Aeryn. Almost out of fuel, he turns to rejoin Moya in order that they may pursue Aeryn, refusing to let her go now that he knows about the baby. Suddenly, a wormhole opens up and swallows Moya whole, leaving Crichton stranded and alone in open space, out of fuel.
- Main article: Season 3 credits
- 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 *.
- Commerce station
- Jocacean Memorial Planet
- Electromagnetic Cluster
- Siren star
- Sacred Leviathan burial space