The crew learn that Scorpius has removed the neural chip from Crichton without their knowing. Even with the chip removed, though, Crichton still has Scorpius's presence in his brain. D'Argo prevents Zhaan from ending Crichton's life. Zhaan and Stark discover that Aeryn isn't completely dead and Zhaan decides to risk her own life to bring back that of her friend.
The station on which Moya's crew was attaining supplies is suddenly and unexpectedly struck by an energy storm. The crew shuffles to save as many people as possible, but soon learn that another storm is heading in their direction. Moya is stuck in the station's docking cables, but eventually learns that the storm is being brought upon the station by the bartender.
When Crichton convinces Moya and crew to make a stopover near a wormhole, another ship lodges itself in Moya. Jool comes out of her cyropod intact, though distraught over the death of her family. Crichton and Rygel try to help with the separation of the ships but are told only one of the ships will make it out of the wormhole.
The crew learns that Moya's rapidly declining condition is a result of the crew of the other ship and work to save Moya. The only hope for them was to be the first ship, aligned to the wormhole when the phaztillon generator is activated and that would require the ultimate sacrifice of one of Moya's crew.
Crichton, D'Argo, Aeryn and Stark find themselves trapped in the past and the rest of Moya's crew look on as their presence has a pronounced effect on the planet below.
Crichton, D'Argo, Chiana and Jool try to find replacement parts on a dying Leviathan only to be faced with a killer that systematically tries to kill and eat each of them. Crichton sees Kaarvok eat D'Argo and Chiana, but soon learns the truth of his friends's fates. Kaarvok clones people and then eats the clones. They escape, but with an extra John Crichton aboard. Moya and the rest of the crew tend to a wounded Talyn.
D'Argo, Chiana and Rygel go to the planet Kanvia for supplies to aid Talyn's regeneration. D'Argo makes a peaceful trade near impossible when he gets into a fight with a high ranking official. Crais awakens to inform the crew how Talyn was beaten. Crichton literally argues with himself over who is the original, but when one of the Crichtons is injured, the other supplies the necessary blood.
Talyn is swallowed by a space creature with Crichton, Aeryn and Crais on board. Crichton learns of Aeryn and Crais's shared past. Crais suggests that Aeryn also be implanted with a transponder to help guide Talyn and goes through with it even though Crichton protests. They decide to rig an explosion with the help of Stark and Rygel (outside on a transport pod) in order to escape the creature.
The crew of Moya find the ship invaded by creatures that can possess bodies. One contacts them through Pilot, claiming to be hunting the other, but then refuses to leave Pilot even after the other rider is outed.
Aeryn's mother leads a retrieval squad to the planet where Talyn is trying to recover. Aeryn and Xhalax don't have a joyful family reunion. Crichton realizes that the retrieval squad is also after Crais.
A peacekeeper prowler arrives with the news that Scorpius is alive and still working on wormhole technology. The pilot, a member of Scorpius' team, asks that in exchange for what she knows about wormholes that she be given Moya.
Talyn nearly runs itself into a sun and, as an aftereffect, a mist permeates the ship and causes the crew to experience amped-up versions of their biggest emotions. It turns out that the sun has a built in siren mechanism. Stark attempts to take control of Talyn to rescue a spirit trapped in the sun.
While on enforced leave from Moya, Crichton and D'Argo find themselves struggling to save Jool and Chiana from too much pleasure.
Crichton is visited by the alien that takes the form of his father and asked why he was sharing wormhole technology. Crichton immediately suspects Furlow, the mechanic that had fixed his Farscape module and the fight on her world leaves Crais and Talyn blinded. Rygel's interrogation reveals Scarran involvement. The Jack alien agrees to help Crichton rid himself of the Scorpius clone once and for all.
Jack and Crichton team up to create a displacement engine to destroy the Scarran ship approaching their location. A Scarran boards Talyn and only Stark's delaying tactic helps save himself and Crais. Furlow double crosses everyone and reveals that she's in bed with the Scarrans and takes the displacement engine. Crichton is able to stop her but not without the consequence of a huge dose of radiation.
When the alien craft aboard Moya malfunctions, D'Argo blames Crichton and in a momentary rage he hits the human, causing severe head trauma. The alien craft, at the same time, initiates a self-destruct sequence. Comatose, Crichton envisions himself and his crewmates as Chuck Jones-style animated characters.
While trying to get over the death of Crichton, Aeryn runs into her father and her mother, though the latter is intent on killing Aeryn. Stark abandons Talyn and his crewmates in pursuit of Zhaan's spirit.
Moya encounters a transport pod full of escaped Peacekeeper prisoners at their planned rendezvous with Talyn. Crichton learns of the death of his twin when Talyn eventually arrives. One of the escaped prisoners proves to be a traitor and broadcasts their location to the Peacekeepers.
Rygel and D'Argo negotiate with Scorpius in an effort for Crichton to infiltrate the Peacekeeper Command Carrier and destroy their wormhole research. Talyn destroys a few Peacekeeper Prowlers but then continues on to attack a hospital ship, killing many innocents.
Crichton infiltrates Scorpius's wormhole research team as the rest of the crew enjoy the amenities of the Peacekeeper Command Center, even if the Peacekeepers themselves don't enjoy the presence of Moya's crew. Moya is attacked and when Crichton and Aeryn confront Scorpius, he reveals it was the doing of a new player -- Commandant Mele-On Grayza.
Crais appears to betray Crichton's sabotage plans to Scorpius but later Crais and Aeryn tell Crichton that it is all part of a new plan. Crais and Talyn would starburst from inside the Command Carrier, destroying it, but also them in the process.
Crichton experiences hallucinations spurred on by Noranti as Moya is attacked trying to put Talyn remains in a Leviathan Burial Space. The crew of Moya appear to go their separate ways leaving Crichton behind.