Episodes 23 - 44
Introduction note: Crichton's voiceover for Season One's opening credits states he is "being hunted by an insane military commander," referring to Captain Bialar Crais, but at that season's end we see Crais virtually acknowledging Crichton's innocence in the death of his brother, and not attempting to kill Crichton at every opportunity. Scorpius assumes Crais' command while Crais chooses to flee in Talyn instead. Crichton's voiceover is unchanged in Season Two's opening credits: we can only assume the military commander hunting Crichton is now Scorpius.
In addition to trying to survive in the Uncharted Territories, the crew of Moya must now concern themselves with eluding Scorpius, discovering the truth about the Ancients, and tracking down the renegade Crais and Talyn. This is further complicated when the neurochip implanted into Crichton's brain to extract the wormhole knowledge he possesses begins to manifest itself as hallucinations of Scorpius (whom he later names 'Harvey' in reference to the imaginary rabbit in the film of the same name starring James Stewart).
As their journeys continue, Zhaan returns to the Delvian Seek and finds comfort in continuing her spiritual training, D'Argo and Chiana grow closer and soon fall in love, while at the same time, Crichton and Aeryn battle their own complicated attraction towards each other. While relaxing on The Royal Planet, the crew comes into contact for the first time with the ruthless Scarrans, a cruel and power-hungry race, who soon learn of Scorpius' interest in Crichton. John is enlisted to marry the crown princess on the planet, being the only male who has DNA compatible with hers. After foiling plots against John by both Scorpius and the Scarrans, the crew leaves the planet, with the princess carrying Crichton's child.
Stark, the Stykera Crichton was imprisoned with while in Scorpius' custody, returns to Moya, becoming close to Zhaan and bringing D'Argo news that his son Ka Jothee is alive and is a slave. The crew is divided. Do they go in search of Talyn? Do they try to rescue Jothee? Do they turn tail and try to get as far away from Scorpius as they can?
Stark suggests a plan to rescue Jothee, as well as a substantial number of his own people, from slavery. The crew will raid a shadow depository, a bank where thieves store their goods. The plan goes awry when the crew's stolen riches turn out to be metal-eating arachnids. As a last resort, the crew must start a fire inside Moya to destroy them, leaving the ship severely crippled. Scorpius purchases the lot of slaves containing Jothee and attempts to divide the crew by offering him in exchange for Crichton. Without currency to pay various hired mercenaries to rescue Jothee, Crichton secretly exchanges himself in the desperate hope that Scorpius can remove the neurochip and the accompanying hallucinations, which have since made him mentally unstable. During the intrigue at the shadow depository, Moya encounters her son Talyn once more.
The crew of Moya rescues Crichton before Scorpius can remove the chip and likely kill Crichton in the process, and they decide to seek out someone who can perform the removal without damaging Crichton, and keep the wormhole information away from Scorpius. They find a Diagnosan to help Crichton and heal the burnt-out Moya. He is located on an ice planet where millions of living subjects, frozen at the point of death, are held in stasis to be used as organ donors. Before they get a chance to perform the surgery on Crichton, the neural clone possesses him, sends out a distress signal to Scorpius, and kills Aeryn. After Aeryn's funeral, the real Scorpius arrives on the planet, reclaims the chip, and leaves Crichton alive but with the speech center of his brain destroyed, condemned to suffer incoherently as payback for all the trouble he has caused. In addition, a remnant of the neural clone remains in Crichton's head - it can no longer control Crichton as the chip did, but it does speak to Crichton and give him advice. Specifically, it wants Crichton to commit suicide so it won't be trapped in his head anymore.
- Main article: Season 2 credits
- Note: The first episode of series 2 was originally to have been a story entitled "Re:Union". It was decided not to air the episode in its original form and "Mind the Baby" became the season premiere. "Re:Union" was reedited with additional scenes and broadcast later in the season as "Dream a Little Dream". In the Farscape collection DVD 'Dream a Little Dream' is placed as the first episode, with no further changes. Netflix does the same, but also flips episodes five and six, and moves ten to follow thirteen.
- 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
- The Barren Planet
- Budong mining colony
- Commerce Planet 03
- Favored planet
- Five Pulsars
- The Mist
- Royal cemetery planet
- Royal Planet
- David Kemper singled out Andrew Prowse for praise on the second season saying "While the directors had finished their episode and moved onto the next one, Andrew was polishing the edit. Andrew did the sound effects and the spotting with the directors if they could make it, or if not, he did it on his own. He did the music, the final edit. He worked on the CGI. He coordinated with the directors, helped resolve their stuff. When you look at the finished eps and marvel at them, you have to marvel at the talent of Andrew Prowse. All that CGI, sound effects and music are the results of the talented people who put them in, and what the director started and brought to fruition. But someone had to sit hour after hour and make the critical decisions – and that was Andrew. Deb Peart did the editing and coordinated, but Andrew sat in the edit room, the music spotting room, and met with the composer. He was the unsung hero of Farscape, far and away." ("Farscape Chronicles" - Starburst Edition DVD v2.3)