Aeryn has managed to rescue D'Argo and Crichton, they're hiding in an asteroid belt. But she needed help from Crais and Talyn to rescue them. Even as she's checking on her friends, she's secretly helping Crais train Talyn. How long can she maintain her secret?
The crew finds a dying Orican, a Luxan holy woman. She asks D'Argo to help her with a ceremony. She tests D'Argo's worthiness, and throws him out saying he's not worthy. He explains to his friends why she rejected him, and convince him to explain it to her. She accepts his help, and starts the ceremony, but instead of dying, she becomes revitalized but her actions cause Moya to suffer.
Upon learning of her brother's death, Chiana leaves Moya in Aeryn's Prowler. Crichton and Aeryn find her on royal burial grounds living with a group of people with some strange customs, including throwing themselves off a cliff. Meanwhile Rigel loots what he can of the burial grounds, but finds the treasure is cursed.
Chiana buys a picture in a store, which is more than it seems. The picture is changes and shows Chiana what will happen to her, when it shows she is on fire, the crew must discover the origins of the picture, and find an old enemy.
While waiting for Moya to pick their Transport Pod, Zahn tells Crichton of Moya's adventures after the Gammeck base was destroyed. Zahn was on trial for murder, with Chiana, and Rygel acting as her defense lawyers.
The crew is attacked by a vessel, Zahn goes over to the ship to negotiate a peace. But the ship attacks again, the attack reacts unexpectedly interacts with the shields causing everyone on board Moya to switch identities, ie Aeryn is now Rygel, Rygel is now Crichton, etc. Now the crew must figure a way to get back to their original bodies.
An energy ball enters Moya, and comes into contact with everyone on board. When it reaches Crichton, it engulfs him, then a cave man comes out, followed by Crichton. Blood tests show the cave man is Crichton. Another Crichton emerges from the energy ball, this one is extremely advanced. The probe says it needs to study at least one of the Crichtons. If it doesn't get at least one of them back, it will destroy Moya.
The crew rests on a planet where the successor to the throne needs a genetically compatible mate to take the throne. She finds her mate ... in Crichton. But someone else wants the throne, and are willing to eliminate Crichton to prevent her rise.
The Queen offers Crichton a choice; marry her daughter the crown princess, or she'll turn him over to Scorpius. Meanwhile, Moya has found her builders, the ones who created Leviathans. They know Moya gave birth to a warship, and do not want another one born. They want Moya to shut down, permanently
Crichton has been turned into a statue. Now someone has cut off his head, and everyone searches for it. Once it's reattached, he finds out he cannot be turned into a statue again, he wouldn't survive, but the Princess is having his child. Meanwhile Z'han tries to convince the builders that Moya is peaceful and should not be killed, failing that she tries to convince Moya not to kill herself.
Chiana returns from a Commerce Planet with a cute little creature called a Vorc that is said to be capable of hunting down parasites which may have inadvertently come on board with the crew's supplies. Aeryn thinks Chiana was swindled; the Vorc appears too scatterbrained and unimposing to hunt parasites even if Moya had parasites - and Aeryn doubts Moya does. But Crichton soon encounters a hostile beast eating its way through one of Moya's walls. However, when he tells the others about the sighting, they are reluctant to believe him. Crichton is having an increasingly...
The crew finds a cloudy area where they might be able to hide from Peacekeepers. Aeryn goes into the area to check it out. She returns a few hours later, much older. And tells them to leave the area. Now they have to figure out how to escape the cloud before they suffer the same fate as Aeryn
A ship is destroyed by Talyn while Moya's crew is aboard. Talyn, with Crais, starburst away while the rest are captured by another ship. Each member of the crew is interrogated in turn. The one who fired the shot will be executed. Who's telling the true version of the events, and will the guilty party be punished?
Rygel and Aeryn return from a planet to Moya accompanied by another Nebari who aims to take Chiana back. The crew is temporarily mind-cleansed except the Pilot but they put a collar on him and thus take over Moya to attain the nearest Nebari territorial post. Chiana learns that her brother is alive. Crichton who is not affected by mind-cleansing thanks to Scorpius' chip, makes Chiana reveal the reason she is being chased: she knows of her people's plot to infect the galaxy with a deadly contagion. Crichton must work together with Pilot and Rygel, quickly recovered due...
D'Argo finally gets a lead on his son, Jothee. He will do anything to get him back, but Jothee will be sold as a slave. They need a lot of money to buy Jothee's freedom. The crew will steal from a depository to get the money they need to free Jothee. Stark, back from the dead, is the author of the plan.
Scorpius bought the lot with D'Argo's son just before Moya arrived and demands Crichton in exchange for Jothee. They plan to buy help of the beings they encountered before to break into repository, for the stolen money. But this money turns out to be alive and eats the ship. Then Crichton makes the ultimate deal.
The crew is going to break into the depository to free Crichton. Crichton is being tortured for wormhole technology. Nothing is going like planned with those mercenaries but unexpected arrival of Talyn helps them to break free. They get rid of Scorpius but their losses are too big, among which Crichton's sanity.
The neural chip in Crichton's head is driving him insane. He pleads with D'Argo to kill him. They take him to a healer to have the chip removed. The chip takes control of Crichton, and someone on Moya will pay the price before Crichton can regain control of his body. Scorpius arrives just after they start the procedure to remove the chip.