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.
D'Argo drags the others on a search for an old, dying Luxan, Nilaam. She turns out to be an Orican - a Luxan holy woman who wants D'Argo to help her die. D'Argo has no choice but to take part in the Luxan death ritual, but as Nilaam starts to cross to the next realm, she sees a chance to alter her fate. Changing the ritual, Nilaam, instead of dying, uses D'Argo's life force and emerges as a beautiful young Luxan. However, it soon becomes clear that the energy she used was not from D'Argo, but from Moya, and the consequences for the living ship are catastrophic.
Distraught at the death of her brother Nerri, Chiana blasts down to a royal cemetery planet and joins a gang of nihilistic young aliens. Crichton, Aeryn and Rygel fly down to the planet to try to talk Chiana into coming back to Moya, but she insists on taking part in a potentially deadly local ritual called "Taking the Stone", a leap into a chasm using sound waves to slow the fall. Crichton tries to intercede, but must realize that this new, aberrant behaviour is something Chiana has to work through herself.
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 Five Pulsars, an intense paranoia affects the crew, turning them violently against each other. Crichton must fight against his own paranoid delusions to work out what Traltixx is actually doing and how to stop him.
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 too refuses to communicate with the crew, not wanting to reveal his own complicity in the murky circumstances surrounding his instatement as Moya's guide.
Chiana returns to Moya with a fortune-telling portrait she picked up from a passing trader. The picture foretells the deaths of the crew, and one by one, they start to die off. Zhaan realises her old foe Maldis, an evil sorcerer, is behind the terrifying goings-on. He is trying to re-corporealise and is feeding on the fears of Crichton, D'Argo, Chiana and especially Zhaan. When Zhaan and Crichton are the only ones left alive, they are forced to travel into the sorcerer's dimension and confront him face to face.
The crew, starving and desperate, head for a mining colony within a giant Budong carcass. When they arrive, they must contend with B'Sogg, the camp's overlord. Each of the crew goes to work in different ways to obtain necessary supplies. When a miner is attacked and killed by the Keedva, a vicious creature that roams the mining tunnels, Crichton soon discovers that B'Sogg, the colony's self-styled Keedva slayer, is in fact controlling the creature. B'Sogg unleashes the Keedva on an unarmed Crichton, leaving him to kill or be killed.
While desperately searching for news of Crichton, the rest of Moya's crew find themselves on the planet Litigara - a world where lawyers comprise ninety percent of the population. Zhaan is jailed for a minor offence - a major complication given that Pilot is having difficulty stopping Moya from StarBursting away to look for Talyn. Zhaan is then unwittingly drawn further into the ugly domestic politics of Litigara when she is framed for murder.
When Moya is attacked by Halos-1, a hostile ship, the crew discovers that rather than being injured, they have all swapped minds. Zhaan, on a diplomatic mission to the alien ship, is the only one unaffected. The Halosians then plant an acidic weapon in Moya's neural cluster, so that not only is the crew in a state of bodily confusion, they must also deal with the acid burning through Moya's circuits. Zhaan, with no way of getting to the crew, must contend with the Halosians on her own.
A mysterious energy sphere implants itself inside Moya and envelops Crichton. When Aeryn fires upon it, it ejects not one, but three Crichtons! One of them is the original, one of them is a de-evolved 'Ape-Man Crichton', and the other is a super-evolved 'Future Crichton'. The energy sphere turns out to be a dimensional portal, and a transmission from this portal demands that unless one of the Crichtons is sent back, Moya will be pulled though in her entirety. It seems obvious to everyone to send the ape-Crichton back, but when he cannot be found, the original Crichton finds himself at the bottom of the evolutionary ladder.
The crew travels to a planet under the rule of a benevolent monarchy. The Queen-to-be, Princess Katralla, has had her DNA altered by agents working for her avaricious brother, Prince Clavor. As such, she cannot find a compatible partner - one of the requirements of becoming monarch. By pure chance, it turns out that Crichton is a compatible partner, and he is encouraged on all sides to marry. Crichton thinks the proposal ludicrous, and Aeryn keeps quiet on the matter, refusing to reveal her hurt feelings. But when Empress Novia threatens to hand Crichton over to Scorpius should he leave Katralla standing at the altar, Crichton consents to the marriage.
Agents working for Prince Clavor try to assassinate Crichton, but their efforts are thwarted by Clavor's fiancee, Jenavian Charto. She turns out to be a secret Peacekeeper Operative on a mission to stop Clavor from taking the throne and making a deal with the Scarrans. Crichton goes into hiding, assisted by the Royal retainer, ro-Na. Meanwhile, Zhaan, Moya and Pilot meet the 'Builder' Kahaynu, one of the Leviathan creators. Angry over the birth of the gunship Talyn, Kahaynu orders nothing less than the immediate death of Moya.
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 Cargn attempt another assassination. Jenavian Charto again comes to the rescue, and she and the restored Crichton escape into the barren lands. Unfortunately for D'Argo, Chiana and Rygel, Empress Novia threatens the execution of every off-worlder on the planet if Crichton is not found. When finding John becomes a life and death matter, D'Argo turns to someone equally desperate to locate the astronaut: Crichton's enemy, Scorpius.
Chiana returns from a Commerce Planet with a cute little creature called a 'Vorc'. When D'Argo is attacked by a vicious beast, the crew utilise the Vorc to track down the unwanted guest. Troubled by hallucinations of Scorpius, Crichton has also been catching glimpses of a ferocious creature eating its way through Moya. The rest of the crew doubt his sanity, until it is discovered that the docile Vorc and the voracious animal Crichton saw are one and the same!
Crichton finds himself back on Earth, apparently safely returned from his failed Farscape mission. Immediately suspicious, Crichton then starts seeing the crew of Moya one by one in various earthbound guises - Aeryn as a doctor, Zhaan as a psychiatrist, even Rygel as an executive. Eventually, Scorpius too appears, but unlike the others, he claims to know what is really going on. He tells John that this new earth is a hallucination created by a Scarran agent, and that in reality, John is a captive. The Scarrans know that Scorpius is interested in John, and through this freakish interrogation technique, they intend to find out why - at the expense of Crichton's sanity.
Returning from reconnaissance near an unknown planet, Aeryn appears on board having aged one-hundred and sixty cycles! After warning the crew that Moya is stuck in time, she then returns to the planet, leaving a desperate Crichton to follow her. Years pass on the planet surface. Aeryn has raised a family and is content with her life, but Crichton is a bitter and disillusioned old man. On Moya, Zhaan and Stark combine their powers to discover that Moya is trapped in a 'Centre Halo', a region where time does not exist.
Crais invites Crichton, Aeryn, D'Argo, Zhaan and Stark on board Talyn, and announces that he is going to remove the young gunship's weapons and replace them with a non-lethal Plokavian weapon called a 'Dampening Net'. When the Plokavians arrive with the device, Talyn suddenly targets and destroys one of their vessels! Crichton and the others are captured after Crais starbursts away with Talyn, and their situation becomes a desperate 'whodunnit'. Each is interrogated in turn by the Plokavians, who intend to execute the person they deem responsible.
Aeryn and Rygel bring onto Moya two Nebari survivors of a Peacekeeper attack, Varla and Melak. Despite their weakened state, the ruthless Nebari manage to mind-cleanse the crew, and in the end only Crichton is unaffected, his mind protected by the Scorpius Clone. Crichton presses Chiana as to the motivations of Varla and Melak. It turns out that Nerri, the brother Chiana though lost, is very much alive, and is now the leader of the Nebari Resistance Movement. The Nebari Establishment knows this, and intends to capture him using Chiana as bait.
Stark returns with a plan to buy the lot of slaves that includes D'Argo's son, Jothee. He proposes that the crew rob a Shadow Depository - a high-security bank for ill-gotten wealth - run by the powerful, insidious alien Natira. An apparent hitch in the plan leads to D'Argo's capture, and though the heist kicks into action, its objective now includes retrieving the Luxan. Incredibly, it transpires that the currency the crew plans to steal belongs to Scorpius, who has just arrived to make a transaction!
Moya's crew escapes the Shadow Depository with the loot, but the shipload of currency turns out to be a horde of insectoid creatures that start to eat Moya! What's more, Scorpius has purchased the enslaved Jothee, completely thwarting Stark's plan. The crew decides to hire mercenaries in order to break Jothee out. Individually, they set out to hire their squad - Bekhesh the Tavlek, Rorf and Rorg the Blood Trackers, Teurac the Sheyang, and Zenetan Pirates led by none other than Rygel's old nemesis, Captain Durka.
Crichton has given himself up to Scorpius in exchange for D'Argo's son, Jothee. The rest of the crew decides to rescue him, hoping also to steal enough loot to pay off the mercenaries. Scorpius reveals to Crichton that he placed a neural chip inside Crichton's brain, a chip that contained a clone of Scorpy's personality. While searching out Crichton's wormhole knowledge, the Clone has been infecting and warping Crichton's identity. So, even as the spectacular rescue gets underway, it seems that Crichton will forever be a prisoner in his own mind.
The crew heads to the icy home of a famous surgeon, the Diagnosan Tocot, hoping he will be able to remove the neural chip from Crichton's brain. However, not willing to give up so easily, the Scorpius Clone takes over Crichton's mind, and a mind-controlled Crichton escapes from Moya. Aeryn takes chase in her Prowler, but a critical mistake plummets her, helpless, into a frozen lake. Crichton finally submits to Tocot for the surgery, but even as he lies on the operating table, it turns out that Scorpius himself has been one step ahead of them all...
