John Crichton. Astronaut. Flung through a wormhole and lost in a galaxy far from home. He finds himself in the middle of a prison break, surrounded by hostile aliens, soaring through space inside a glorious living space ship called Moya. Hunted by the relentless Peacekeepers, he allies himself with his unimaginably alien fellow refugees and searches for a way home.
Continuing work on his theories of wormhole technology, Crichton ekes out an existence on board Elack; an old, dying Leviathan. The peace is shattered by the intrusion of a female alien, Sikozu, and a squad of Grudek mercenaries intent on harvesting Elack's neural tissue. Crichton fights to save his new home, his struggle hindered by the Grudeks' pet: a vicious and deadly alien canine called the Brindz Hound.
Crichton, Chiana and Rygel are reunited with D'Argo and Jool at an archaeological site run by Jool's people, the Interions. The purpose of the dig is to find a missing probe that might reverse the planet's dangerous atmospheric conditions. Peacekeepers led by Grayza land and capture the crew, and Crichton finds himself unable to fight back, mysteriously compelled to do Grayza's bidding.
D'Argo and Sikozu come up with a plan to crash Elack onto the Peacekeeper pursuit craft, facilitating their escape. Crichton is forced to consort further with Grayza to ensure success. When the plan goes awry, the crew begins a search for the probe that will reverse the planet's deadly atmospheric conditions, but a most unexpected enemy stops them in their tracks.
After a forced landing, the crew is divided by an eloborate trap that leaves Crichton, D'Argo, Noranti and Rygel underground in a lava-filled system of caves. Chiana and Sikozu are left outside, trying to re-activate D'Argo's ship. Inside, Crichton and the others are hunted down by mercenaries who are not only protected by energy shield belts, but are led by a monster impervious to the fiery lava.
Crichton and the crew are reunited on Moya. Crichton finds Aeryn suffering from Heat Delirium and under the care of Scorpius, who wants asylum aboard Moya. Soon after, a giant Lukythian ship appears nearby, and its Captain, Ullom, claims that Aeryn was recently part of a team that assassinated an important Lukythian leader. Ullom offers to heal Aeryn in return for information about the plot. While battling with the notion of trusting Scorpius, Crichton remains unaware that neither Aeryn nor Ullom is telling the whole truth.
Crichton correctly predicts a wormhole's appearance near Moya, but simultaneously a giant space plant captures the Leviathan. An attack with D'Argo's ship only succeeds in sending the plant into Moya's conduits, making it even more difficult to kill. Eventually, an agent is found that will repel the plant, but it only exists in Scorpius' cooling rods. In order to save Moya, Crichton will have to place trust in his arch nemesis.
Chiana and Crichton are sucked into a game world ruled over by a virtual Stark, who sends Crichton on a quest to 'Kiss the Princess'. To escape the game, they are forced to battle old friends and enemies in fantastic guises. Meanwhile, aboard Moya, Scorpius escapes and brings the crew under his control.
When Moya is raided by bounty hunters working for the Peacekeepers, every crew member is captured except for Crichton and Noranti. The armoured intruders shrink the captives and imprison them inside holding cavities in their torsos - if Crichton harms them, he endangers his friends as well. Finding that Scorpius is also free and on the run, Crichton teams up with him to fight off the menace, unaware that the leader of the bounty hunters has a hidden agenda.
The crew lands on a planet divided by generations of clan war. After experiencing strange hallucinations, Aeryn is subliminally coerced into assassinating a clan leader. When Crichton also starts having hallucinations, they must uncover the planet's political machinations in order to prevent more killings.
While in quarantine high above the patriarchal planet Khurtanan, the crew shares a meal of alien mollusks and almost instantaneously suffers a violent physical reaction. Each crew member becomes bodily linked to one of the others, Crichton to Sikozu, Aeryn to Rygel, and so on. It soon becomes clear they have been deliberately poisoned by the local doctor and are being blackmailed in exchange for the cure.
Crichton is sucked down a wormhole he correctly senses will appear near Moya. Within "wormhole limbo" he is confronted by an interdimensional being who is intent on discovering why Crichton was entrusted with this knowledge. The alien sends Crichton through various "realities" of past events to illustrate how dangerous it can be if wormhole knowledge is misused.
The crew travels through a wormhole to Earth, 1985, and Crichton finds he has somehow disastrously changed the course of time; his father Jack is now slated to fly the doomed Challenger mission. Lying low in Crichton's home town, the 'aliens' use the timely Halloween celebrations to remain (almost) anonymous, while Crichton tries to revert the timeline, in the process putting his younger self in mortal danger.
The crew returns to Moya, in orbit around modern-day Earth, to find Jack and a contingent of Earth dignitaries waiting for them. The aliens are introduced to an amazed and apprehensive public, but soon find life in the public eye difficult. As Crichton tries to readjust to life on Earth, his relationships become strained, especially with Aeryn. Meanwhile, a monstrous assassin sent by Grayza hunts for Crichton, and will stop at nothing to accomplish its mission.
Chiana purchases Talikaa, an abused slave girl from a passing Trading Ship. When the crew starts acting strangely and Talikaa goes missing, they realize she may not be as innocent as she first seemed. The crew tracks down the Trading Ship only to find its occupants have succumbed to a painful death, the result of neural harvesting by an alien arachnid. When it is revealed that the arachnid is Talikaa's true form, Moya's crew must hunt down Talikaa before they suffer the same fate.
Scorpius takes Crichton, D'Argo and Rygel into an advanced training camp where students learn mental discipline. D'Argo is confronted with the arrival of Macton, the Peacekeeper who murdered D'Argo's wife, Lo'Laan, then framed him for the crime. When Scorpius forces Crichton into torturous anti-Scarran training, D'Argo must face the demons from his past alone.
While purchasing a camouflage device for Moya, Aeryn and Sikozu witness the nearby landing of a Peacekeeper squad led by Grayza and Braca. Chiana and Noranti choose to undergo genetic manipulation to elude the searching Peacekeepers. Aeryn and Sikozu spy on Grayza who has convened a secret meeting with Scarran emissaries. Aware that the meeting could have catastrophic consequences, Aeryn decides to assassinate Grayza.
Having overheard Ahkna mention the secret Scarran base known as Katratzi, Sikozu is sure this is where the Scarrans intend to take their captive, Aeryn Sun. Though Moya's data banks have no record of Katratzi, Crichton's sure he's heard the word "Katratzi" somewhere before, if only he could remember where. Unable to sleep, Crichton pores over a documentary intercepted from Earth that examines the visit by "aliens" and discovers that the documentary just might hold the key to locating Katratzi.
Aeryn is being held captive aboard a Scarran freighter captained by Jenek, who's determined to find out if Aeryn's carrying Crichton's child. To discover the location of the Scarran base where Aeryn is being taken, Crichton and Scorpius travel through a wormhole to a mixed-up "unrealized reality" version of Moya. As the others wait for their return, pursuing Peacekeepers draw closer.
Moya's crew tracks Aeryn to a Scarran Border Station, where the freighter she is imprisoned upon is about to leave for Katratzi, a Scarran base. To keep the ship docked and under quarantine, Noranti gives Rygel a deadly, contagious disease. Though this gives the crew time to come up with a plan to rescue Aeryn, they do not figure on the cunning and ruthlessness of Aeryn's Scarran captor, Jenek.
Moya's crew travels to Katratzi, a Scarran base where Scorpius is being tortured for wormhole information. The base is home to both Kalish and Charrid forces - underlings for the Scarrans. The crew plans to incite a confrontation between these two contingents, hoping this diversion will allow them to free Scorpius, and prevent wormhole knowledge from falling into Scarran hands.
After thwarting Crichton's escape plan, Scorpius denies that he's a Scarran spy, and demands Crichton's help to destroy a cavern of vital Scarran flora claiming it will also provide them with a better means of escape. And while Rygel and Noranti fight an evil Stark, Sikozu must reveal her true colors if they are all to survive.
Now safely back on Moya, Crichton learns of the Scarrans' intention to invade Earth. He feverishly analyzes his wormhole data and comes up with a way to collapse the wormhole to Earth, but the method is not one that he can implement alone. Meanwhile, Braca demands Scorpius be released from Moya and returned safely to his Command Carrier and Aeryn has a few surprises of her own, including the identity of her baby's father.