The crew come across a ship that is molecularly de-stabilizing. D'Argo makes everyone bring it aboard when he discovers that there are Ilanics on board. Crichton goes on to the escape pod he gets a shock and starts experiencing strange visions of the future, firstly of himself and Matala, then of Moya's destruction.

The crew find an old abandoned peacekeeper ship adrift in space, on board they discover that Crais was there recently where he deposited a unit of techs to make repairs. Meanwhile Rygel learns that this was the ship where he was first held captive and starts getting paranoid. Things get even worse though when a group of fire breathing aliens show up.

Crichton comes across the same conditions that initially created a wormhole. He leaves Moya in his module with Aeryn where he attempts to create a wormhole and return home. Although a wormhole forms it is unstable and the module gets damaged and he is forced to make an emergency landing on the planet to make repairs. On the planet he and Aeryn encounter a holographic message sent by Crais, offering rewards for: D'Argo, Zhaan and Rygel.

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.

A peacekeeper ship is approaching Moya, so Crichton and Aeryn pose as peacekeeper officers on a secret mission while everyone else gets locked into cells to make the deception seem realistic. The peacekeepers that come aboard have some secret cargo. But when their secret cargo escapes, no one on board is safe.

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.

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.

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.

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.

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

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.

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.

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

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

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

While on a transport pod, Chiana nags Crichton to try out a virtual reality game. A transmission comes through from D'Argo concerning a problem with Scorpius. Despite this, Chiana pulls Crichton into one of the games, where they become trapped, and the only way out is to complete the game.