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 brain.

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 recalcitrant about revisiting her past - especially her relationship with Velorek, the man charged with forcibly bonding a new Pilot to Moya. Pilot two refuses to communicate with the crew, not wanting to reveal his own complicity in the murky circumstances surrounding his installment as Moya's guide.

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.

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.

Scorpius buys the slaves containing D'Argo's son before D'Argo can. Some of the crew leave Moya in search of mercenaries to rescue Jothee. Meanwhile back on Moya, the stolen money has turned into metal eating spiders that begin to consume Moya.

An alien ship fires a weapon at Moya. Although the energy shield is active, some of the blast makes it through and causes everyone's consciousness to jump into another body.

Now married, Crichton and Katalla 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. The crew must save John and Chiana while escaping Scorpius.

Moya arrives at a planet where the population 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.

The Scorpius clone puts John into a dream world to prevent the Scarrans from getting any wormhole knowledge.

The crew returns from a Commerce Planet with a load of Crackers and a meek alien called Traltixx, who promises he can alter Moya's electromagnetics 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 Traltixx is actually doing and how to stop him.

Princess Katralla's mother brings in Scorpius promising Crichton that if he doesn't marry her daughter, she will hand him over. Meanwhile, Prince Clavor starts a plot to assassinate Crichton so that he may ascend to the throne instead of his sister.

A temporal distortion traps Aeryn and John on a planet's surface, where they live out the rest of their lives -- while Moya remains trapped in orbit, experiencing only hours. Stark returns to the ship with news of D'Argo's son.

A Nebari group come aboard 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.

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, Crichton decides to remove Crais from control of Talyn. Scorpius finally sees his chance to strike.

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. Note: This episode features after the "Look at the Princess" trilogy on the DVDs.

Crais and Talyn return. The crew are put on trial for an attack that Talyn made on an alien ship.

Maldus returns to torment the crew, convincing them that their friends have perished. One by one, the evil sorcerer drags them into his realm.

The crew bring aboard an alien tracker to remove some creatures that came aboard hidden in some cargo.

With Moya out of food, Chiana leads everyone to a dead boudong where she once worked.

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.

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.

Chiana leaves Moya and goes to 'grave planet' populated by reckless thrill seekers who play dangerous and life threatening games.