The crew find a doctor that can heal Moya's burns and remove Crichton's neural chip. Things are complicated however when Crichton is informed he needs additional brain tissue from a donor in stasis who will die when the tissue is removed. Also Scorpius is beginning to take over Crichton's mind.

Crichton turns himself over to Scorpius in order to free Jothee. With all the mercenaries now aboard Moya, the crew form a plan to rescue Crichton and destroy the depository.

The crew is stunned when they learn that Scorpius has bought the slaves out from under D'Argo. Rather than trade Crichton for Jothee, Crichton, D'Argo, Aeryn and Rygel seek out mercenaries to help them steal the slaves. In the process, they encounter some enemies they've fought in the past. Meanwhile, back on Moya, the stolen money has turned into metal-eating spiders that begin to consume Moya.

Stark returns to Moya with a plan to rob a shadow depository and buy a contingent of slaves, one of which is D'Argo's son Jothee. D'Argo attempts the robbery on his own however and now the crew must recover him as well as the money they require.

A group of Nebari come on board Moya and attempt to mind cleanse everyone using a drug. Pilot and Rygel are the only two who can resist the effects. Crichton also remains unaffected due to Scorpius' neural clone.

When Crais and Talyn rendezvous with Moya, the crew boards Talyn, where Crais presents them with a proposal about the young ship's future. Meanwhile, a ship that Crais intended to purchase weaponry from approaches Talyn, butTalyn fires and destroys it. Crais and Talyn flee, but the crew get captured and are put on trial for for their lives.

Moya gets stuck in a temporal anomoly but is unaware of it. Aeryn returns from recon after only a few hours but has aged many years.

Crichton wakes to find himself back on Earth and the Farscape project failing. However, all is not as it seems, with D'Argo, Aeryn and co. co-existing with DK and his Dad. Crichton only has Scorpius to turn to for answers before it's too late!

When the crew hear rumors of creatures infesting ships in the area, they buy an alien tracker to remove the creatures aboard Moya. But it soon becomes apparent that the creatures could cause a lot of damage before the tracker finds it putting the crew in danger.

Now married, Crichton and Katralla are frozen into living statues so that they may watch over the presiding governments of the next eighty cycles. Immediately, Clavor and the Scarran emissary attempt another assassination and succeed in removing Crichton's head. Empress Novia threatens to kill all off-worlders, putting D'Argo, Chiana and Rygel in danger. Finding Crichton's head is now a matter of life or death.

Plots swirl around Crichton and his fiancee, Princess Katralla. The empress promises Crichton that if he doesn't marry her daughter, she will hand him over to Scorpius. Meanwhile, Prince Clavor plots to assassinate Crichton so that he may ascend to the throne in his sister's place.

Moya arrives at a planet where the people test their genetic compatibility by kissing. Crichton kisses a princess, who is next in line for the throne, and discovers that his DNA is a perfect match for her. He must now marry her and they will rule together. This is against the wishes of her brother, who is second in line for the throne -- conspiring with a Scarran.

A strange globe appears on Moya, sucking in Crichton and duplicating him creating two additional people. One who is a de-evolved 'cave man' and another who has increased mental ability.

When a hostile alien ship fires first at the Moya, the crew, despite the fact that their energy shield is up, finds their minds switched into another person's body. As a result, Crichton is in the body of Aeryn, Aeryn is in the body of Rygel, and Rygel is in the body of Crichton. In the cockpit, Pilot is in the body of Chiana, Chiana is in the body of D'Argo, and D'Argo is in the body of Pilot. They're all forced to adapt to their new bodies as they attempt to figure out what caused the switch.

While waiting inside a transport pod, to be picked up by Moya, Zhaan tells Crichton about being accused and tried for murder during his absence.

With Moya out of food, Chiana leads everyone to a dead Budong where she once worked. Meanwhile on Moya, Aeryn is left to deal with a carnivorous Zhaan.

While visiting a planet Chiana visits a trader and is given a picture which can supposedly predict the future free of charge. Back on Moya the crew become alarmed when the picture begins to predict people's deaths and soon the crew are unable to stop it. But before long it is revealed that an old enemy is responsible for what is happening.

A datacam tape is uncovered showing Aeryn as part of a Peacekeeper firing squad that executed a previous Pilot aboard Moya. The rest of the crew wants answers but Aeryn is reluctant to revisit her past - especially her relationship with Velorek, the man charged with forcibly bonding a new Pilot to Moya. Pilot (the current one, that is) refuses to communicate with the crew, not wanting to reveal his own complicity in the murky circumstances surrounding his installment as Moya's guide.

The crew returns from a commerce planet with a load of crackers and a meek alien called T'raltixx, who promises he can alter Moya's electromagnetic profile in order to make her untraceable. Crichton is skeptical; it seems too good to be true. As they pass through a constellation of pulsars, an intense paranoia affects the crew, turning them violently again each other. Crichton must fight against his own paranoid delusions to work out what T'raltixx is actually doing -- and how to stop him.

After getting word that her brother is dead, Chiana leaves Moya and goes to a 'grave planet' populated by a race of young people who play dangerous and life-threatening games.

D'Argo takes part in a sacred ritual that helps an old Luxan, an Orican, to survive. During the ritual the Orican draws energy from who she thinks is D'Argo but is actually Moya. Consequently Moya starts to age rapidly.

Crichton, Aeryn and D'Argo are stranded in an asteroid field while Scorpius searches for them. Their safety depends on Crais, who is nearby in Talyn. Aeryn teaches Crais how to control the young Leviathan - the only thing she can offer in return for the lives of her friends. When Moya returns to the asteroid field to look for her offspring, and Crichton decides to remove Crais from control of Talyn, Scorpius finally sees his chance to strike.