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.

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.

D'Argo and Rygel meet Braca and Scorpius in a cafe to conduct negotiations when it is unexpectedly attacked.

Moya takes Talyn's remains to the sacred burial ground where D'Argo is forced to destroy a rogue Leviathan that is attacking other ships.

Crichton, now aboard a dying leviathan named Elack, encounters an alien named Sikozu who aids him in stopping the Grudeks who are intent on obtaining toubray (Leviathan neural cluster tissue).

Elac arrives at the planet where D'Argo, Jool and Old Woman are investigating the ruins of an ancient civilization.

Crichton must find the third probe to end the magnetic summer, while avoiding Grayza and Oo-Nii.

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.

D'Argo, Rygel, Crichton, Chiana and Sikozu get back to Moya only to find that Scorpius is there waiting for them along with Aeryn, now suffering from heat delirium. Aeryn has granted Scorpius asylum and claims that Scorpius saved her life.

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.

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.

A group of bounty hunters come aboard Moya and take everyone hostage. When Crichton arrives back with the Old Woman he destroys the bounty hunter's ship and goes aboard Moya to rescue everyone while the Old Woman puts herself into a coma where she can survive outside the ship.

Moya arrives at a planet where Aeryn gets accused of murder.

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.

Crichton falls into a wormhole and meets up with a strange man who shows Crichton the consequences of wormhole travel.

After accidentally returning to Earth, Crichton discovers it he is in 1985 and he has altered the time line, causing his father to be scheduled to fly on the doomed shuttle 'Challenger'.

Moya arrives at Earth in present day, Christmas. The crew show their ships and technology to Earth's scientists. Crichton starts writing a journal. The creature left on board Moya by Grayza manages to get to Earth where it starts killing and hunting down Crichton.

Moya takes on a new passenger, Talikaa, when Chiana insists upon it. However Talikaa turns out to be an alien creature in disguise and is intent on harvesting the crew's neural energy.

Scorpius signs D'Argo, Crichton and Rygel up for a training camp where the students learn mental discipline by battling in an artificial environment.

The women of Moya travel to a dead Leviathan to buy a sensor beacon for Moya which will allow her to appear to be a different ship. While there Aeryn and Sikozu spy on a secret meeting between the Peacekeepers and the Scarrans.

Crichton watches a documentary that Moya receives from Earth about their recent visit showing interviews with Crichton's relatives and other people who interacted with the crew.

Crichton and Scorpius travel to one of the 'unrealized realities' where Crichton believes he heard Stark say "Katratzi." Meanwhile on a Scarran ship, Aeryn resists torture.

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 the option to leave on the Peacekeeper Command Carrier no longer available and his nuclear bomb disarmed, Crichton must follow Scorpius' plan and destroy the Crystherium Utilia.

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.

60 days on and Rygel is retrieving pieces of John and Aeryn from the sea bed. The diagnosan (Season of Death) 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.

With Sikozu's help, everyone manages to escape from the Scarren prison. Joining up with D'Argo, Jothee, Chiana and other Luxans they cripple and leave the Scarren ship and return to Moya. Crichton returns to the wormhole where he gets Einstein to give him the ability to build a wormhole weapon.