The journey has never been easy for lost American astronaut John Crichton, the escaped alien prisoners who are his friends, or their living ship, Moya. And in the third season the ride becomes wilder than ever when powerful issues of love, loyalty, and sacrifice loom large.
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.
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.
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.
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.
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.
Moya rendezvous with Talyn who is seriously damaged. They hide in the atmosphere of a planet to prevent the Peacekeepers from finding them. D'Argo and Rygel go down to the planet to find some Clorium, a drug that will help Talyn recover.
Talyn is swallowed by a boodong, leaving Stark and Rygel stranded in a transport pod.
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.
Talyn lands on a planet covered mostly with vegetation that will help him to heal. Crichton, Aeryn and Crais leave the ship in search of Xhalax.
Scorpius puts the neural chip into his own brain in an attempt to retrieve vital wormhole equations from Crichton.
Talyn gets the urge to fly into a sun. While in its vicinity Stark is contacted by an alien women who is being held against her will.
Crichton, D'Argo, Jool and Chiana are forced to take a holiday by Pilot as he is fed up with their constant bickering.
Crichton must seek out an old friend who has gained too much knowledge about wormholes.
Jack (The Ancient) unlocks the wormhole knowledge in Crichton's mind so together they can build a device to destroy the Scarran dreadnought.
There is an accident while D'Argo is demonstrating what his ship can do. He blames Crichton and knocks him out. In his unconscious state Crichton has some animated dreams.
Aeryn goes to a planet in search of someone who can contact her father.
A group of escaped prisoners come aboard Moya followed shortly by Aeryn, Stark, Crais and Rygel who have finally returned from Talyn.
D'Argo and Rygel meet Braca and Scorpius in a cafe to conduct negotiations when it is unexpectedly attacked.
Crichton goes to the command carrier to sabotage Scorpius' wormhole research.
Crais gets Talyn to starburst inside the command carrier, causing it to collapse in on itself.