Astronaut John Crichton attempts to use the Earth's atmosphere to propel his module at high speeds. He is hit by a radiation wave and is sucked through a wormhole into a distant part of the universe--straight into the middle of a space battle.
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.
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.
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 visits a planet full of happy workers. Soon D'Argo and Zhaan start working and refuse to return to the ship. Meanwhile Rygel's body fluids become explosive and Aeryn and Pilot must learn why before Rygel dies.
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.
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.
A scientist extracts DNA from several of Moya's crew, promising them that with it he would be able to use it to find the location of their home planets. Things get more interesting however when he asks for some of pilot.
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.
While on a transport pod piloting lesson with Aeryn, Crichton gets caught in an energy field which is invisible to their sensors. Back on Moya, a strange guest docks and comes aboard to warn the crew about The Flax, an invisible energy net created to catch ships.
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.
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.
Crichton is sucked down a wormhole and crash lands on a beach...on Earth, Australia. Although the home he has returned to isn't as real as it seems. Everything gets worse when the rest of Moya's crew shows up and are experimented on...killing Rygel.
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.
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.
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.
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.
Rygel steals a transport pod and goes to the peacekeeper command carrier to betray the others. However he ends up returning to Moya with Crais who wants asylum. Crichton decides to destroy Scorpius' Gamac Base to give Moya time to escape.
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.
D'Argo takes part in a sacred ritual that helps an old Luxan, an Orican, to survive. During the ritual the Orican draws energy from who she thinks is D'Argo but is actually Moya. Consequently Moya starts to age rapidly.
Chiana leaves Moya and goes to 'grave planet' populated by reckless thrill seekers who play dangerous and life threatening games.
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.
Maldus returns to torment the crew, convincing them that their friends have perished.
With Moya out of food, Chiana leads everyone to a dead boudong where she once worked.
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 strange globe appears on Moya, sucking in Crichton and duplicating him creating two additional people. One who is a de-evolved 'cave man' and another who has increased mental ability.
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.
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.
The crew bring aboard an alien tracker to remove some creatures that came aboard hidden in some cargo.
John Crichton is back on Earth but things are very different.
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 important news.
Crais and Talyn return. The crew are put on trial for an attack that Talyn made on an alien ship.
A Nebari group come aboard Moya and attempt to mind cleanse everyone using a drug.
Stark returns to Moya with a plan to rob a shadow depository and buy a contingent of slaves, one of which is D'Argo's son Jothee. D'Argo attempts the robbery on his own however and now the crew must recover him as well as the money they require.
Scorpius buys the slaves containing D'Argo's son before D'Argo can. Some of the crew leave Moya in search of mercenaries to rescue Jothee. Meanwhile back on Moya, the stolen money has turned into metal eating spiders that begin to consume Moya.
Crichton turns himself over to Scorpius in order to free Jothee. With all the mercenaries now aboard Moya, the crew form a plan to rescue Crichton and destroy the depository.
The crew find a doctor that can heal Moya's burns and remove Crichton's neural chip. Things are complicated however when Crichton is informed he needs additional brain tissue from a donor in stasis who will die when the tissue is removed. Also Scorpius is beginning to take over Crichton's brain.
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.
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 mad scientist.
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.
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 Elac, 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 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.
