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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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.

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.

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.

D'Argo and Stark try to heal John, left with his head open on an operating table, while Scorpius attempts to avoid discovery. Zhaan makes a great personal sacrifice, while Jothee and Chiana commit an indiscretion.

Moya docks at a commerce station so the crew can spend some of the money they acquired from the depository. Disaster strikes however when the station is hit by a storm.

Moya approaches a wormhole, gets pulled in and fused to another ship.

The crew work out a way of getting free from the other ship and out of the wormhole. Things become more complicated when their new 'friends' begin to sabotage Moya and Crichton picks up a transmission from Earth.

Stark accidentally sends himself, Crichton, Aeryn and Jool back in time where they alter the time line and are forced to interfere further to restore it.

In need of supplies, Crichton lands his transport pod on a dying leviathan which is full of hungry cannibals and a scientist who has the ability to create clones.

Moya rendezvous with Talyn who is seriously damaged. They hide in the atmosphere of a planet to prevent the Peacekeepers from finding them. D'Argo and Rygel go down to the planet to find some Clorium, a drug that will help Talyn recover.

Talyn is swallowed by a boodong, leaving Stark and Rygel stranded in a transport pod.

The crew of Moya start blacking out and missing portions of time. Pilot becomes inhabited by another entity who needs to 'taste' each crew member to determine if they too are being inhabited.

Talyn lands on a planet covered mostly with vegetation that will help him to heal. Crichton, Aeryn and Crais leave the ship in search of Xhalax.

Scorpius puts the neural chip into his own brain in an attempt to retrieve vital wormhole equations from Crichton.

Talyn gets the urge to fly into a sun. While in its vicinity Stark is contacted by an alien women who is being held against her will.

Crichton, D'Argo, Jool and Chiana are forced to take a holiday by Pilot as he is fed up with their constant bickering.

Crichton must seek out an old friend who has gained too much knowledge about wormholes.

Jack (The Ancient) unlocks the wormhole knowledge in Crichton's mind so together they can build a device to destroy the Scarran dreadnought.

There is an accident while D'Argo is demonstrating what his ship can do. He blames Crichton and knocks him out. In his unconscious state Crichton has some animated dreams.

Aeryn goes to a planet in search of someone who can contact her father.

A group of escaped prisoners come aboard Moya followed shortly by Aeryn, Stark, Crais and Rygel who have finally returned from Talyn.

Crichton goes to the command carrier to sabotage Scorpius' wormhole research.

Crais gets Talyn to starburst inside the command carrier, causing it to collapse in on itself.

D'Argo and Rygel meet Braca and Scorpius in a cafe to conduct negotiations when it is unexpectedly attacked.

Moya takes Talyn's remains to the sacred burial ground where D'Argo is forced to destroy a rogue Leviathan that is attacking other ships.

60 days on and Rygel is retrieving pieces of John and Aeryn from the sea bed. The diagnosan (Season of Death) re-crystalises them and they start getting to know the species that live on that world. Meanwhile, Scorpius and Sikozu are aboard a Peacekeeper Command Carrier on a recon mission. They attack a Scarren ship which provokes the Scarrens into declaring war on The Peacekeepers.

With Sikozu's help, everyone manages to escape from the Scarren prison. Joining up with D'Argo, Jothee, Chiana and other Luxans they cripple and leave the Scarren ship and return to Moya. Crichton returns to the wormhole where he gets Einstein to give him the ability to build a wormhole weapon.