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.
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 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.
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.
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.
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.
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.
Zhaan is tried for murder on a litigious planet. "Re:Union" was originally filmed as the Season 2 premiere, but was held back and "Mind the Baby," the second episode, was broadcast first. This allowed the fates of Crichton, Aeryn, and D'Argo to be more quickly resolved after the cliffhanger ending of Season 1. New opening and closing scenes were filmed for '"Re:Union," making it a flashback. The episode was renamed "Dream A Little Dream" and broadcast later in Season 2 (02x08). The original edit of "Re:Union" went unseen until June 1, 2001, when it aired as a special presentation in the U.S. on the Sci Fi Chanel.
Crichton, Aeryn and D'argo are stranded in an asteroid field while Scorpius searches for them. Their safety depends on Crais, who is nearby in Talyn. Aeryn teaches Crais how to control the young Leviathan - the only thing she can offer in return for the lives of her friends. When Moya returns to the asteroid field to look for her offspring, Crichton decides to remove Crais from control of Talyn. Scorpius finally sees his chance to strike.
The crew returns from a Commerce Planet with a load of Crackers and a meek alien called T'raltixx, 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 against each other. Crichton must fight against his own paranoid delusions to work out what T'raltixx is actually doing and how to stop him.
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.
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.
This hour long documentary was aired before series 3. It was hosted by Ben Browder, Claudia Black, Rygel and Pilot. It featured clips from the previous 2 sereis' and gave an overview of the show and got viewers up-to-speed with the current storyline. Getting any new viewers ready for the next series.
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.
60 days on and Rygel is retrieving pieces of John and Aeryn from the sea bed. The diagnosan re-crystalises them and they start getting to know the species that live on that world. Meanwhile, Scorpius and Sikozu are aboard a Peacekeeper Command Carrier on a recon mission. They attack a Scarren ship which provokes the Scarrens into declaring war on The Peacekeepers.