It is now clear that this group has bonded together. D'Argo and Crichton are 'allies.' Zhaan (Virginia Hey) feels great responsibility for the welfare of the group. Aeryn and John have grown closer. Even Chiana (Gigi Edgley) works with the others - in fact, she and Rygel (Voice Jonathan Hardy) save Zhaan from a death sentence in the episode 'Dream A Little Dream.' By mid-season, Chiana and D'Argo have embarked on a love affair.
But season two soon reveals itself. Regardless of everything John Crichton has achieved, Scorpius did something to him in the Aurora Chair that will ultimately cost him his sanity.
The audience first gets a glimpse of this in the demented 'Crackers Don't Matter.' An alien on board Moya causes paranoia and violence among the group, but only Crichton hallucinates visions of Scorpius. As time goes on, Crichton sees and hears more of Scorpius, especially when he is under physical or emotional stress.
In 'Won't Get Fooled Again,' known to the cast and crew as 'Episode 14,' Crichton seems to be back on Earth again. This time, he doesn't believe it. It is a hallucination induced by a Scarran who is torturing him to get him to reveal what Scorpius wants. In this episode, a copy, or clone of Scorpius reveals himself to John. Scorpius put a neural chip in Crichton's head to retrieve the wormhole technology John may have learned from the Ancients in 'A Human Reaction.' The clone is supposed to burrow in and search for it, not revealing himself. But the clone pops out when Crichton is in jeopardy of death himself, or when John tries to kill the real Scorpius. The chip prevents Crichton from killing Scorpius at the end of the third part of 'Look At The Princess.' The clone saves Crichton in 'Won't Get Fooled Again,' and later in 'A Clockwork Nebari.'
The audience starts to suspect that something is wrong with Crichton as hallucinates Scorpius. They find out about the chip in 'Won't Get Fooled Again.' Crichton himself doesn't know what is wrong until Scorpius tells him during 'Liars, Guns and Money.' Crichton's descent into what seems to be madness is really the clone taking over his personality. John is willing to give himself up to Scorpius during the second part of 'Liars, Guns, and Money.' While his friends rescue him temporarily, he cannot save himself. Finally, in 'Die Me, Dichotomy,' the clone of Scorpius takes over completely, and John sees Scorpius, not himself, in the mirror. In fact, the audience is looking at Ben Browder in the full Scorpius makeup. It is the clone in Crichton that injures Zhaan and Jothee (Matt Newton), and finally causes Aeryn to crash over a frozen lake and drown. When Crichton's personality reasserts itself after the shock of her death, he is willing to let a surgeon try and remove the chip, even though he may die or suffer permanent brain damage. It seems that the surgeon is able to remove the chip, but causes Crichton to lose parts of his memory and function. The surgeon is going to try and restore everything, but with John's brain open, Scorpius comes in, kills the surgeon and takes the chip. John is left lying on the table without the power of speech. And so ends season one.
In summary, season two of Farscape is the time during which Scorpius causes Crichton to go insane, by putting a clone of himself in a neural chip inside Crichton's brain. The clone seems to have accessed the wormhole data Scorpius wants before the surgeon removes the chip - as the doctor works, John experiences memories, and visions of wormholes appear next to the chip. The audience has no idea how functional Crichton might be come season three. Who is there to help restore his brain?
Aeryn lies in a pod on the surgeon's icy planet. She drowns after John causes her Prowler to crash into an icy lake. Just before that, she declares her love for him. In fact, the entire second season Aeryn develops more and more feelings for Crichton. In 'The Locket' he is revealed to be the love of her life. Crichton looks at her in death and says that he loves her. How will he live with what he did?
D'Argo and Chiana get involved in an unlikely, very physical love affair, but they are very different. D'Argo finally finds his son and gets him back in 'Liars, Guns, and Money.' Jothee, who is half Sebacean and half Luxan, has mutilated himself and gone through hell. Even though he seems happy to see his father, it is not an ideal reunion. Jothee finds Chiana very, very interesting.
Chiana has helped the group many times, but also has shown her tendency to run away under stress. She and Rygel make quite a pair, trying to steal things or get off the ship when things get bad. Chiana learns that her brother Nerri is heading a resistance movement among the very evil Nebari, and wishes she could join him. She seems interested in Jothee, too.
Rygel is still self-absorbed, and very happy that the group acquired wealth from the shadow depository they robbed during 'Liars Guns and Money.' But surprisingly, he is willing to give away his loot to pay for treatment for a badly burned Moya.
During the three part 'Look At The Princess' trilogy, everyone but Zhaan and Pilot went down to see the royal wedding and got mixed up with the royal family. Moya felt a familiar signal, and found the place of her makers, her god Kahaynu (Jonathan Hardy). Kahaynu says he must kill Moya, because she gave birth to a gunship. Pilot, bonded to Moya, will also die. Zhaan tries to talk him out of this. Finally Moya comes back to life. The Kahaynu was testing Zhaan, not Moya, and tells her she must guard Moya. That becomes a main priority for Zhaan. Stark, another inmate of Scorpius' cell on the Gammak Base who escaped first season with Crichton, returns in 'The Locket.' He turns out to be a noncorporeal life form taking corporeal form, and so when he is dispersed as a punishment in 'The Ugly Truth' he is able to come back later in 'Liars, Guns, and Money.' He and Zhaan begin their own affair.
Scorpius chases Crichton all season. He retrieves his chip, and presumably the wormhole technology he wants to use as a weapon. His clone seems to have accomplished his mission.
Crais, who will always be a warrior, has spent all season alone on Talyn. It is very unclear, even at the end of the season, whether or not he or Talyn is the more aggressive. Talyn is a formidable gunship, capable of destruction. Both he and Crais invite Aeryn to join them, but sadly, she dies before making such a decision.
Everyone, at the end, is deciding what to do next. Talyn is trying to help Moya recover from her burns. Zhaan, perhaps with Stark, will stay with Moya and Pilot. D'Argo wants to go someplace peaceful with Chiana and Jothee, both of whom want something more exciting, maybe each other. Crais is mourning Aeryn aboard Talyn. Rygel has booked passage away from the area. They are waiting to hear of John's treatment - not knowing that Scorpius has left the surgeon for dead and the damaged Crichton to live in torment.
Season Three will begin with 'Season Of Death' on March 16th on the Sci-Fi Channel at 9PM (check local listings). It will be preceded by a Farscape special which will help bring viewers up to speed.