Crichton pulls Crais away from Talyn where the exiled Peacekeeper was trying to gain control of Moya's child. When Moya moves in on Talyn, it asks for the return of Crais. The situation becomes more tense with the imminent arrival of Scorpius.
D'Argo learns that a Luxan is living on a nearby planet. The holy women requests D'Argo's help in performing a ritual of passing, but he provides enough energy for the woman to renew herself. A possible catch to the situation arises when Moya's body starts to break down.
Upset over the apparent death of her brother, Chiana leaves Moya and finds companionship among a group called the Clansmen who live reckless lives and perform tests that constantly put their lives in danger. Aeryn and Crichton try to talk Chiana out of taking a fateful leap.
The crew bring a mechanic on board Moya in an effort to install some stealth technology to protect them from Scorpius. However, when they attempt to make the leap to his home planet, the crew is affected by pulsars and find themselves battling each other.
Rygel gives Pilot a tape from his bonding with Moya that reveals that Aeryn had a hand in the ill fate of Moya's previous Pilot.
Chiana returns to Moya with a picture that seems to predict her own unhappy future, including her death. The picture, however, is the resting place of the previously defeated sorcerer Maldis who seeks revenge upon Zhaan.
The crew suffers through a food shortage, but the lack of meat has a truly averse effect on Zhaan. Zhaan begins to grow buds that cause allergic reactions in her fellow crewmembers. While others are off attaining food, Aeryn tries to alleviate Zhaan's stress with light but only succeeds in causing the release of spores that effect both Aeryn and Moya, the latter to a dangerous degree.
During the time when Talyn, Crichton, Aeryn and D'Argo were missing, Zhaan runs into trouble on a planet (Litigara) filled with lawyers. When no one is willing to defend her, Chiana and Rygel step up to the plate only to learn that they could share a fatal verdict along with their client.
When Moya comes under fire, they decide to raise the defense shield they savaged from the Zelbinion, but wake to find that the crew has swapped bodies. Zhaan, a prisoner of the enemy ship, learns that the enemy is firing on Moya in retribution for an attack they suffered from Talyn.
A mysterious sphere enters the ship and lingers above Crichton. Aeryn uses the opportunity to shoot it. The sphere expands and engulfs Crichton. He emerges from the sphere but eventually so do two other versions of Crichton, one seemingly up the evolutionary ladder and the other down. Adding to the scare of the multiple Crichtons was the dimensional pull of the sphere.
While on the Royal Planet, it's discovered that Crichton is compatible genetically with a princess who needs to find a suitable mate in order to take the throne. D'Argo cuts a deal with Scorpius that guarantees the rest of the crew freedom if Crichton proceeds witht he marriage. Crichton eventually learns that he will be turned into a statue for 80 years after the ceremony.
Prince Clavor attacks Crichton in an attempt to prevent his sister from attaining the throne. Even when he seemingly escapes the planet, Crichton lands in the hands of Braca. Eventually, Crichton is rescued and all is made right, if one considers the marriage he doesn't want and being frozen as a statue for eighty years right.
While Aeryn tends to injuries received while rockclimbing, Crichton is turned into a statue and then has his head stolen followed by the disappearance of his remaining body. D'Argo teams with Scorpius to find Chiana before a Scarran does, but they arrive second. The Empress Novia proclaims death to all off-worlders when she learns of her son's death.
Crichton sees a beast roaming through Moya, but because of hallucinations, the crew doesn't believe him until they see the creature themselves. D'Argo is poisoned during at altercation with the beast. The crew use a Vorc they brought on ship to get rid of parasites to try and find the beast so they can work up an antidote.
Crichton once again finds himself on Earth and introduced to people with startling similarities to the crew of Moya. He immediately questions the validity of the world and finds the only voice of reason, the only person who wants to help him escape, is none other than Scorpius.
When Aeryn checks to see the safety of hiding from Scorpius in a mist, she vanishes only to return later much older, claiming to have lived a full life (including grandchildren) on a planet that exists on the other side of a rift.
The elation Moya feels at the reappearance of Talyn (with Crais) is of short duration when Talyn destroys a Plokavian ship and starbursts away leaving Moya and crew to try to make peace with another ship searching for its comrades.
Aeryn and Rygel return to Moya after a mind-cleansing by the Nebari. It turns out that the Nebari were after Chiana for information that would lead to her brother (who apparently had ties to the rebellion). After the crew is mind-cleansed, it's up to Crichton and Pilot to stop the Nebari from gaining control of the Universe.
Stark returns to the ship after being apparently eradicated with news of D'Argo's son, Jothee. Stark comes up with a plan to rob a depository in order to buy the slaves of which Jothee was a member. Their plan is met with complications when Scorpius arrives at the bank.
In an effort to gain control of the party, Scorpius purchased the lot of slaves and executed all of them except for Jothee. Scorpius then offers Jothee in exchange for Crichton. To outmanuever Scorpius, the crew hire bounty hunters, but to their dismay, the money they planned to use was actually a parasitic trap.
Crichton gives himself up to Scorpius for Jothee's release. Aeryn re-enlists the mercenaries to rescue John. Talyn arrives to help aid Moya's recovery from burning out the parasites. The escape plan hits a snag when Scorpius captures and interrogates one of the mercenaries.
A Diagnosan is employed to heal Moya from her recent injuries and it is suggested that the neural clone Scorpius implanted in Crichton could also be removed. Crichton finds himself controlled by the neural clone and is responsible in the apparent death of Aeryn. Crichton decides to forego risk and undergo the removal procedure, which is eventually interrupted by the real Scorpius.