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.

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.

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

Moya arrives at Katratzi. Crichton attends the peace talks between the Scarrans and the Peacekeepers ...with a nuclear bomb.

With the option to leave on the Peacekeeper Command Carrier no longer available and his nuclear bomb disarmed, Crichton must follow Scorpius' plan and destroy the Crystherium Utilia.

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.

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.

Moya arrives at a station where the Scarran vessel transporting Aeryn is docked.

With their Crystherium stores low, the Scarrans must travel to Earth through a wormhole as those flowers grow there. With Pilots help, Crichton tries to collapse the wormhole leading back to Earth.

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.

Moya arrives at Earth in present day, Christmas. The crew show their ships and technology to Earth's scientists. Crichton starts writing a journal. The creature left on board Moya by Grayza manages to get to Earth where it starts killing and hunting down 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.

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

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

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.

After accidentally returning to Earth, Crichton discovers it he is in 1985 and he has altered the time line, causing his father to be scheduled to fly on the doomed shuttle 'Challenger'.