Crichton lies on the operating table with the neural chip removed, unable to communicate. Aeryn is cryogenically frozen. The surgeon is able to restore Crichton's ability to speak. A dormant patient awakens and goes after everyone. Zhaan attempts to revive Aeryn, but at a very high cost.
The crew relaxes on a space station. D'Argo wants to propose to Chiana, but something will affect his relationship with those closest/dearest to him. A fanatic has a device to attract solar storms, and wants to destroy the station. The crew must find a way to save the station
The crew searches for a planet where they can plant Zhaan, so that she can recover. They encounter a wormhole and stop to investigate. A ship emerges from the wormhole and collides with Moya. Now the two ships are merged together, and stuck inside a wormhole. The two crews must find a way to separate the ships, but if they separate, only one ship will survive.
The two ships are still linked together. The crews are being attacked by a strange creature, Moya's taking a heavy beating. Crichton finds a transmission from Earth. The ships will finally be separated, with one of the Moya crew making the Ultimate sacrifice.
Moya's crew tries to relax on a planet. A device unexpectedly reacts with Stark, and they get sent back in time. The crew must figure out a way to get history back on course, but their actions in the past have repercussions.
Upon arriving at the rendezvous coordinates with minimal life support in their transport pod, Crichton, D'Argo, Chiana, and Jool are forced to dock with a nearby Leviathan bearing a Peacekeeper control collar. They find the Leviathan is incredibly sick and its pilot is unresponsive, but cannot easily find the needed parts for repair.
The crew tend to Crais and Talyn. Both are badly injured. The 2 Crichtons try to adjust to life with each other. The crew gets embroiled in a political situation while trying to buy supplies for Talyn's recovery. Crais tells Aeryn the Peacekeeper Recovery Unit attacking Talyn is led by Aeryn's mother.
While Rygel and Stark are out scouting the area, Talyn, still recovering from the Peacekeeper attack, is swallowed by a Budong. John and Aeryn attempt to "lay anchor" by catching grappling hooks on the Budong's ribs. Meanwhile Stark and Rygel have a near miss with the Budong and attempt to find out what happened to Talyn.
Upon passing through an electromagnetic cluster, Crichton sees a strange being aboard Moya. It seems to attack him, causing him to black out and bleed profusely. However he cannot prove his experience actually occurred, so the rest of the crew believes he is hallucinating. He continues to have these episodes, but without the help of his friends he has little chance of discovering what is happening to him.
While Talyn is resting on a planet with high gravity he senses the retrieval squad, led by Aeryn's mother, setting down nearby. John, Aeryn, and Crais head out to confront the Peacekeepers and keep them away from Talyn while he recuperates.
Scorpius puts the neural chip in his head to unlock the wormhole knowledge in the chip. He shows his origin to residual memory of Crichton that's been embedded in the chip in an effort to gain his support. Meanwhile the Moya crew encounter a scientist who has been working with Scorpius on wormhole technology.
Back on Talyn, John is trying to figure out whether Crais let Aeryn's mother, Xhalax, live in order to save his own skin, but is interrupted when Talyn goes head first towards the nearby sun. Talyn manages to pull himself from his course, but endures radiation damage. As the crew splits up for damage control, Stark notices a vapor flowing through the ship and begins to hear voices. John and Aeryn, at work repairing some of Talyn's systems, become increasingly flirtatious with each other, but stop after noticing the vapor as well.
D'Argo and Crichton are constantly arguing with each other. Tired of the arguing, Pilot banishes both of them from Moya for 10 days. They return to Moya sooner than expected. They tell them of their adventure planet side, and hope that Pilot understands that they're no longer welcome on that planet.
A wormhole appears near Talyn. Crichton realizes it's "Jack" the ancient whom he encountered earlier. The ancients have found a new home, the ancients are worried about the misuse of wormhole technology. He needs to see if Crichton is worthy of the knowledge, by investigating Furlough, who has built her own Farscape module.
Jack now trusts Crichton, and has unlocked the wormhole knowledge in Crichton's head. Now they race to build a weapon to fend of approaching Scarrans. But an opposing force is even closer waiting for an opportunity to strike, there will be causalities and the survivors will be severely affected.
D'Argo injures Crichton, as Crichton lies in a coma/near death, he escapes into a highly animated world. It's Farscape, Chuck Jones/Loony Tunes style. Meanwhile D'Argo's actions create a crisis on Moya, which could destroy the Leviathan
Aeryn is devastated. She leaves Talyn, and grieves on a planet. Talyn's crew tries to help but she doesn't want their help. She spots someone who might be her father. But not all family reunions are joyous.
Moya and Talyn's crew reunite at last. Aeryn is still getting over her loss, and cannot face Crichton. Moya rescues some Peacekeeper prisoners but at least one of them still works for the Peacekeepers. Stark gives Crichton a message from the deceased Crichton. He gives his twin a mission.
Rygel and D'Argo meet with Scorpius and Braca to negotiate a deal, so the crew can board the command carrier. Two would-be robbers interrupt the bargaining process, now they're forced to work together to find a way out of their predicament.
The crew has been captured, Crais betrayed them. Now Scorpius is threatening Earth. Crichton must help him develop wormhole weapons or he'll wipe out Earth. Crichton has no choice but to help him. One person will make a decision that will stop Scropius's research, but a high price will be paid.
Moya wants Talyn's remains in a sacred Leviathan place. But another Leviathan won't allow it. The crew's last mission together is to help fulfill Moya's wishes. After that, everyone goes their separate ways. Crichton discovers a secret of Aeryn's.