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.

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.

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.

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.

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.

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.

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.

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.

Chiana leaves Moya and goes to 'grave planet' populated by reckless thrill seekers who play dangerous and life threatening games.

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.

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.

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.

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

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.

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.

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.

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.

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

When stopped off on a planet, Rygel leaves the rest of the group and is caught in an unbreakable orange substance while stealing treasures he discovers in a cave. When D'Argo, Crichton and Noranti go looking for him, the cave seals them in. Two huge grunts appear who have protective armor which protects them from weapons fires.

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.

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

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

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.