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.

Moya gets infested with bugs who have come on board to breed. They turn up the temperature to speed up the process but this causes Aeryn to get heat delirium as she is cold blooded. The bugs seem to be able to replicate members of the crew. And as if that isn't enough, a peacekeeper ship shows up.

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.

A group of Tavleks come aboard for trade negotiations. Rygel takes a vitally important crystal from Moya to make himself seem wealthy. The Tavleks kidnap Rygel and take him down to the planet, leaving one of their wounded on board. Everyone goes to the surface to get him except Zhaan who stays on board to keep an eye on the Tavlek left behind.

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.

The crew visits a planet full of happy workers. Soon D'Argo and Zhaan start working and refuse to return to the ship. Meanwhile Rygel's body fluids become explosive and Aeryn and Pilot must learn why before Rygel dies.

A peacekeeper beacon goes off and Moya has to land on an alien planet to prevent it's signal being intercepted and Moya being discovered. Crichton, D'Argo and Aeryn leave Moya and explore the planet in search of a substance that can be used to numb Moya's senses so the beacon can be removed. Crichton gets separated from the group and meets up with some inhabitants of the planet who hide him from the authorities.

Crichton is put into a head-to-head battle with Crais by a magical being named Maldis who feeds off the emotions of others and makes himself stronger by absorbing all of the negative energy and anger from Crichton and Crais.

A scientist extracts DNA from several of Moya's crew, promising them that with it he would be able to use it to find the location of their home planets. Things get more interesting however when he asks for some of pilot.

During routine searches for Peacekeeper beacons, D'Argo falls down a chute, destroys a Peacekeeper shield and gets ejected into open space. After being rescued D'Argo starts to think that everyone on Moya are members of his family. Moya, meanwhile, starts to alter the environmental conditions inside the ship so that it is hardly habitable for the crew. .

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.

While on a transport pod piloting lesson with Aeryn, Crichton gets caught in an energy field which is invisible to their sensors. Back on Moya, a strange guest docks and comes aboard to warn the crew about The Flax, an invisible energy net created to catch ships.

Moya responds to a distress call from another pregnant Leviathan. On arrival at a planet they are contacted by a Delvian who informs them that the distress call was a deception. It was her way a getting Moya to come to them. The Delvians have a hidden agenda though. They want to forcefully take Zhaan's knowledge and learn how she overcame her insanity.

Crichton leaves Moya in his module for a drive. Moya starbursts leaving Crichton marooned and alone in space. He finds a planet and makes it his home where he lives for several months until the others find him. He is unwilling to accept however, that Moya didn't starburst intentionally.

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.

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.

Moya tries to starburst to prove to the crew that she still can. It goes slightly wrong though and she gets stuck in starburst and split into several different dimensions.

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.

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.

Moya is hiding from a peacekeeper command carrier in an asteroid field. The crew receive a distress call and Crichton, Zhaan and D'Argo go down to one of the asteroids to rescue a women who has an unusual appetite.

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.