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

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.

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.

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.

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

Crichton and Chiana try to infiltrate a peacekeeper base to get some vital medicine for Aeryn. Crichton gets caught by Scorpius and imprisoned. He is tortured using a device called the 'Aurora Chair' which is able to look inside his mind and where Scorpius learns that Crichton has the secret to creating wormholes.

Scorpius attempts to extract the wormhole technology from Crichton's mind, while Aeryn mounts a rescue operation. Crais finds himself at Scorpius' mercy, and Moya gives birth.

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

Crichton is sucked down a wormhole and crash lands on a beach...on Earth, Australia. Although the home he has returned to isn't as real as it seems. Everything gets worse when the rest of Moya's crew shows up and are experimented on...killing Rygel.

Rygel steals a transport pod and goes to the peacekeeper command carrier to betray the others. However he ends up returning to Moya with Crais who wants asylum. Crichton decides to destroy Scorpius' Gamac Base to give Moya time to escape.

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.

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.

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

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.

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.

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

Astronaut John Crichton attempts to use the Earth's atmosphere to propel his module at high speeds. He is hit by a radiation wave and is sucked through a wormhole into a distant part of the universe--straight into the middle of a space battle.

When a Starburst goes badly wrong, Moya collides with a Nebari ship. On board is Durka, Rygel's former torturer, who has been mind cleansed and now serves the Nebari. Chiana, an attractive young rebel faces the same fate. Rygel takes it upon himself to take revenge on Durka and ends up undoing the cleansing and restoring him to his former, tyrannic incarnation.

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.

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

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.

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.

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.

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