Crichton is rescued from the Leviathan graveyard by a dying Leviathan. He also meets Sikozu who seeks out health food in the form of Leviathan neural cluster tissue. Crichton and his newfound friend are eventually rescued by Rygel and Chiana who inform him of their mutual presence on Grayza's most wanted list.
Crichton finds Moya and more friends at a planet decimated by three probes. Crichton dreams of the location of the third probe which might help save the planet, but they soon have a Peacekeeper command carrier as company. Crichton falls prey to Grayza's secret weapon which involves her femininity.
Even as the planet's magnetics approach critical, Crichton purposefully becomes Grayza's prisoner. Rygel convinces Elack the Leviathan to crash into the planet and ruin the Peacekeepers' ride. The only chance for the crew to survive was to trust Crichton's dream, find the third probe and return the planet to its normal existence.
Rygel's greed lands the crew in trouble when he stumbles along booty and the booby traps left with it, trapping Rygel, D'Argo, Noranti and Crichton with a bunch of thieves.
Aeryn is found adrift in space and suffering from Heat Delirium with Scorpius. The person who takes responsibility in Aeryn's illness insists that she was part of a team that murdered their leader. Scorpius once and for all removes Crichton's neural clone. Scorpius informs the crew of Moya that Braca was approaching them with a missile that can kill Leviathans.
Crichton predicts a wormhole, but then Moya is attacked by a large space plant. Aeryn tells Chiana she's pregnant but unsure of the father.
Crichton and Chiana finds themselves trapped in a virtual reality game that they must beat in order to free themselves.
Moya is attacked and most of her crew is captured, shrunk by the invaders, and placed on the person of the bounty hunters in an effort to protect them from attack.
Aeryn finds herself controlled by hallucinations caused by insects on a planet. Soon, she is also joined by Crichton and the two must fight off the mind control or become each other's murderer.
A doctor that boards Moya to declare the crew well enough to visit the planet below poisons the crew with food and demands a huge payoff. Crichton and Rygel dress up like women to infiltrate a club.
Crichton is pulled into a wormhole by a being from another dimension bent on killing him before his knowledge of wormholes endangers more than just one universe.
Crichton finds himself floating in a space suit above the Earth. He's rescued by his friends only to find out that it is the Earth in 1986. Crichton has to a way to prevent his father from accepting a mission on the Challenger which would lead to his death, but in doing so, accidentally gets his younger self killed.
Crichton and Moya's crew are treated like celebrities on Earth. Aeryn discovers that an assassin has followed them to Earth putting Crichton and all of the people he cares about at risk.
The crew of Moya find themselves acting awkwardly after they purchase a slave girl in order to free her. At first the begin showing bold personalities, but on second touch, they begin to waste away. Only Sikozu remains unharmed and it's up to her to ensure the safety of her shipmates.
Crichton, D'Argo, Rygel and Scorpius attend a mental arts training camp at Scorpius's request. Scorpius wants John to train to be able to resist Scarran interrogation. D'Argo finds the brother of his dead wife at the camp and his belief that Macton killed Lo'Laan becomes muddled by Macton's claims of hyper rage.
Moya's women find themselves in a heap of trouble when they try to secure a sensor distorter for Moya. They stumble upon a secret Scarran/Peacekeeper meeting. They then have to rescue Grayza and Braca before the Scarrans can learn that the Peacekeepers have no wormhole weapons, leaving them quite open to attack.
Crichton learns that Aeryn has been captured by the Scarrans and taken to a very secret base named Katratzi. The name strikes a familiar chord with only Crichton, but he can't place his finger on why.
Crichton agrees to give Scorpius wormhole technology if Scorpius can help Crichton retrieve Aeryn from the Scarrans. He and Scorpius travel to an alternate reality to learn the location of Katratzi. The only hitch to the plan is to get the information Crichton will have to facilitate the death of one of that reality's inhabitants.
The crew of Moya track Aeryn to a Scarran border station and are able to keep her there when Rygel pretends to be sick. When it seems that his ruse may fall apart, Noranti actually gives Rygel the disease he claimed to have putting everyone at risk.
Crichton learns that Scorpius never removed the neural clone and now has wormhole equations while in captivity at the hands of the Scarrans. Crichton returns to the Scarrans wearing a portable nuclear bomb. Other members of Moya's crew attempt to create a riot in order to cover Scorpius's prison break.
Scorpius stops his own prison break, resulting in Crichton and crew being held by the Scarrans. Scorpius informs everyone of the Scarrans dependence on the crystherium flower and that its only location was on Katratzi. Backed into a corner, Sikozu reveals her true nature and kills a Scarran squad through radiation emission. Crichton leaves his nuclear bomb with the precious flowers.
Braca informs Crichton and the rest of Moya's crew that the Scarrans plan on invading Earth to retrieve the flowers destroyed on Katratzi. Crichton discovers a way to fold a wormhole in on itself and permanently close it.