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 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.

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.

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.

The crew returns from a Commerce Planet with a load of Crackers and a meek alien called Traltixx, 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 again each other. Crichton must fight against his own paranoid delusions to work out what Traltixx is actually doing and how to stop him.

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.

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.

A temporal distortion traps Aeryn and John on a planet's surface, where they live out the rest of their lives -- while Moya remains trapped in orbit, experiencing only hours. Stark returns to the ship with news of D'Argo's son.

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.

In need of supplies, Crichton lands his transport pod on a dying leviathan which is full of hungry cannibals and a scientist who has the ability to create clones.

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.

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

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.

While in close proximity to a wormhole, Moya is preoccupied and doesn't notice a slowly moving object heading towards her. Moya collides with the object which then covers her entire hull, causing great discomfort to her as well as the crew.

The crew consume food, sharing amongst themselves. Although if not ingested by the same person, it becomes toxic. They must quickly find a cure or they'll die.