The Commonwealth vessel Andromeda, captained by Dylan Hunt, responds to an urgent distress call to find itself lured into a trap. Nietzschean warships surround them and open fire. Captain Hunt, in a last ditch effort, evacuates the ship and maneuvers toward a nearby black hole. Hunt's first officer, Rhade, a Nietzschean himself, betrays Hunt and attempts to kill him, but Hunt perseveres, killing Rhade in the process. Time dilation near the black hole slows time for the Andromeda and Dylan until a freighter tows it out 300 years later. Dylan now must fight off the band...
Captain Dylan Hunt attempts to drive the invaders from his ship. He manages to scare Gerentex off, but he leaves many of his employees behind. He takes the Maru and uses it to send the Andromeda, still without engine power, on a course back into the black hole. The remaining scavengers work with Dylan to regain engine control and break free from the gravity well. Once free, they regain control of the Maru from Gerentex and Dylan invites the survivors to join his crew and reestablish the Commonwealth.
Trance gets Beka and Dylan to medbay, while Rev goes to see a man about his god and Tyr and Harper are injected with Magog eggs and tied up. Dylan and the Andromeda avatar go down to get Tyr and Harper, leaving Beka behind with orders to use a nova bomb to detonate the "bound" planets' sun in three hours. Meanwhile Rev meets with Bloodmist, and begins to give into his bestial nature. The two of them confront the Magog "god", which seems to convince Rev to kill his friends. Bloodmist takes him to Tyr and Harper, but its a trick and Rev kills Bloodmist. Dylan and Andromeda are overwhelmed when Beka launches the nova bomb, but the Magog "god" manages to absorb all the energy. The distraction gives them time to free Tyr and Harper and get out of there. Trance manages to remove Tyr's spider eggs, but the procedure would kill Harper. He has to take medication to keep them in check, but the medicine won't work forever. Meanwhile, they've figured out that the Magog travelling "bound planets" w
After discovering Tyr has hidden the remains of Drago Musevini on board the Andromeda, Dylan questions Tyr's loyalty. Beka and a Nietzchean both race to repair their ships before the other destroys them, and Harper is left in command of the Andromeda, and must decide whether or not to protect a convoy and risk losing the Andromeda.
The crew watches Rev Bem's fairwell message, not sure whether or not to pursue him, or let him leave. Dylan says that they should respect Rev's decision to leave, but Harper snaps at Dylan and storms out. He is upset because Rev had promised to remove the Magog larvae from his gut. He writhes in pain, but when he tries to take his medication, it has no effect, as the larvae have grown immune to it, as Trance and Rev had warned him they would. Soon after, Harper enlists in Chief Technical Director Hohne's help, as well as the other Persieds. Harper plans to build a machine that will fold space to remove the eggs, but it's affecting time, as well.
As Dylan, Rommie, Tyr and Harper flee from the Ogami, they encounter a ship sent from Earth to explore space over 3000 years ago. As the ship is a giant engine, it travels so fast that the crew never age. As the Maru has no slipstream engine, Dylan is faced with a decision that could change the future of the commonwealth. Can the Andromeda come to the rescue?
After rescuing some people from a storm, a 'maggot' is brought onto Andromeda. This maggot chews through the systems and activates an old hologram of a crew member. This member had sealed himself in one of the hidden decks before the event horizon and had some through it. Believing that Dylan has betrayed the Commonwealth, an avatar and android of the crew man takes over the ship to bring Dylan to justice...
Tyr receives a communication from a human on an abandoned planet and leaves to meet her. As he does, a mad scientist boards the Andromeda using dark matter ninjas. After beating them, the man introduces himself. He loves the woman Tyr is with and wants to kill her, if he cant have her, nobody can. After saving her, he forgives her and lets her live. The episode ends with Tyr revealing that she is actually a Neitzian, the last female from Codiac, Tyrs pride. He says that he wants them to start a new Codiac pride but she refuses and Tyr leaves.
When Dylan is invited to the launch of the first Commonwealth ship made in 307 years, you can tell something will go wrong. As the ship explodes sabotage is suspected. As Dylan and the crew try to find the culprit, they encounter many different suspects while being attacked by a violent pride. Can Dylan find the culprit before the Maru is next?
When an old flame of Beka's is arrested on a planet where only the truth is told, its up to the Andromeda and her crew to save the day. After repeatedly lying, Beka gets nowhere -- so she breaks the suspect out and flees to the Andromeda. As the story unravels, it seems that all is not as it seems...
As the Andromeda responds to a distress call from a planet on the brink of destruction, the crew intercept a transmission from a ship returning to the surface. After seeing the message from Rev Bem the crew loads up to save him from the planet. As Rev is following the path of the Divine flashbacks occur of the Andromeda crew to help him on his way.
When the Andromeda responds to a request to destroy atmosphere generators on Samsarra, they encounter a battle group of Pyrians and stand off until the Commonwealth fleet arrives. in a revelation from Trance, Dylan finds out that Trances people believe the Pyrian fleet stronger and better equipped to handle the forthcoming war. With this information, she tells Dylan to pull out and let the Pyrians win so that they can take on the Magog World Ship instead of the renewed Commonwealth. Dylan sees that the only way to stop them is to destroy the planet that he is trying so hard to save....
After receiving a message from an unknown planet 3 days in Slipstream away, the crew of the Andromeda take it upon themselves to save the people. The strange thing is that the message is a woman and it is going directly into Dylans head and no-one else can hear it. As they enter the ice moon of one of the planets, they come upon the Vault of the Heavens. A large palace made of ice. in discovering this the comm is cut and on Dylan's orders, Tyr destroys an energy cloud above the planet. After discovering that the aliens mean no harm, Dylan finds out that they need the cloud, or the entire species will die! Will they be able to return the cloud before the time runs out?
When the Andromeda is attacked by the Dragons to receive the bones of Drago Mussevni something seems array. Dylan then discovers that Tyr has united all of the Neitzian people under his son, the genetic reincarnation of Drago Mussevni. Will Tyr make the right decision and help the crew of the Andromeda or lead his new people into battle?
The governing body of the Commonwealth has voted "no-confidence" in triumvir Tri-Jema, she sends Dylan to get the Andromeda refitted and visit an augur, who is told to be infallible. This augur, dubbed Citizen Eight, aims to take Tri-Jema's place as triumvir and, according to the triumvir, remove Dylan from command of the Andromeda. The robots sent to the Andromeda to start pre-upgrade repairs turn against the crew, forcing Dylan and Harper to shut them down. Dylan must deal with Citizen Eight before he can bring down the Commonwealth from within.
Dylan is sent on a mission by a triumvir, but is not well informed of the danger he faces. After a haphazard reentry from slipstream, the Andromeda is captured by a gravity field projected from the moon that is the target of their mission. Dylan discovers that the moon is the base of Kroton, a half-human, half-android genius that created the Magog world-ship. Dylan attempts to take out Kroton along with the new weapon he has developed.
The Andromeda investigates the site of a reported Nietzschean attack on a Commonwealth battleship, but find no debris and no sign that any conflict occurred there, much less the reported destruction of a High Guard vessel. Dylan is invited by the Nietzschean rulers of the planet to visit and accepts, but in his descent a solar storm hits the planet, causing his escorts to fall behind. Dylan must deal with the Nietzscheans in order to uncover the truth of what happened in orbit.
After taking a wrong turn in slipstream, the Andromeda receives a distress call from a Commonwealth prison, experiencing a riot the likes of which they have not seen before. Dylan and his crew quickly put down the rebellion, but Dylan keeps having flashbacks to the last time he was on this planet. Romy discovers that a now missing prisoner was not recorded in the logs, implying that she was a mole. Harper is shown the source of the planet's power and is told to bypass the ancient security system guarding it, so that the warden can keep it safe elsewhere. Meanwhile, ...
The Andromeda encounter 2 ships with depleted engines and weapons. They come from a planet, where the two sides have been fighting for as long as anyone can remember. One side is suffering from a disease, they claim the other side is using biological weapons, but the other side says they didn't do it. When Dylan becomes infected, the crew must figure out the source of the virus to save the captain.
Rommie has become too emotional, the Andromeda cuts off her access and runs a full diagnostic to bring the avatar under control, this takes away many of the ship's resources. The Magagog are attacking the crew must defend Andromeda without aide from the AI. Even if they succeed in defending the ship, they may lose Rommie.
The Andromeda rescues a defenseless ship from former Commonwealth fighters. The inhabitants are an Ambassador and his pilot, returning to Arkology from successful peace negotiations with the Magog on board the World-Ship. However, the treaty is revoked when the ambassador dies from the Magog hatching in his stomach. The pilot, a Nietzschean from a supposedly extinct pride, leads the Andromeda to Arkology, a place of peacefulness in all aspects of life, to warn them of the coming Magog attack.
With the Magog World-Ship at hand, Dylan must defend Arkology as one of the Paradine, beings said to have witnessed the creation of the universe. Beka makes her decision to leave the battle while she still can. Harper and Rommie attempt to get Arkology slip-capable again before the World-Ship destroys it.
Beka decides to leave the crew to fight for themselves, but after all of the promises that everyone will be reunited, Trance tells them that they will never be as they are again. When the Magog Worldship finally re-encounters the Andromeda after two years, Rommie and Harper race to take the Arkology to slipstream, Rhade must teach the inhabitants to defend themselves, and Dylan and Trance fight off the invading Magog. But as the Andromeda becomes covered in swarmships, Trance tells Dylan that he--and only he--may escape this alive.
Doyle is plagued by nightmares, and half remembered dreams of life on board the Andromeda. But she was never a member of the crew. One person notices her perceptions are off and realizes Doyle doesn't know who she really is and tries to get her to join with him and others of their own kind. Doyle will learn the truth of her origin, and why she feels at home on the Andromeda.
Beka receives a message from Virgil Vox, the radio personality, concerning a secret from her past. She follows his instructions to a secluded community, where she impersonates a dead child, who would be about her age now. Her "father" reveals that he has been guarding a secret and that it is now time for him to pass it on to her.
While Rhade are busy defending refugees on Seefra Five from the army of a local warlord, Dylan is surprised to find Hohne, the Perseid scientist lost and assumed dead during the problems with Haprer's tesseract machine, tesseract onto the command deck of the Andromeda. Hohne and Harper attempt to recreate the quantum teleporter in order to resupply the pinned-down refugees and during the reconstruction receive a message from the research station near the black hole where the device first worked.
Beka, Harper, Rhade, and Doyle are searching for Vedran treasure. They find a door that is rumored to hold inside a test that if passed will yield great wealth, but if failed will cause madness. Rhade opens the door and follows Beka inside, but Harper and Doyle are left behind as the door shuts behind the pair. Trance teleports to a carnival on Seefra Two to attempt to uncover more of her lost memories. Dylan goes in search of her, while Harper and Doyle attempt to free Beka and Rhade.
Harper discovers a program built into the Seefra system that can destroy eight of the planets, likely as a defense mechanism. Dylan begins plans to evacuate the eight planets, but is interrupted by a new arrival through the Route of Ages. The rest of Trance has returned to remake Tarn-Vedra, but the mechanism designed to that is not working.
While Harper develops a way to save the Seefra system from its impending doom, a spy has slipped on board the Andromeda. Dylan, Rhade, and Trance all feel that someone who should not be aboard is, but cannot confirm their suspicions. Things turn south when the spy attacks Beka by opening a portal to open space inside the ship.
When the blinking sun of the Seefra system goes dark for an extended period of time Dylan takes the opportunity to study the workings of the artifice in the hopes of finding a way of fixing the broken sun. Harper discovers a maintenance protocol built into the sun by the Vedrans that will allow a further extended period of time to study the sun.
Dylan is gravely wounded in a lab accident, but wakes up in the bar with Harper telling bad jokes. He is confronted by a man who is wielding Dylan's force-lances and delivers a cryptic message. After a quick fight with Dylan, the man drops to the floor without apparent cause, but returns in the guise of Rhade to catch Dylan off guard, killing him swiftly. Dylan awakens on med-deck but finds that he has returned just after the accident and does not remember Trance.
Dylan deals with the residents of Seefra One who are unhappy with the number of refugees arriving on their planet. While Beka evacuates Seefra Five she detects a ship full of Nietzscheans headed towards the dying planet; however there have never been any Nietzscheans in the Seefra system with the exception of Rhade. Harper and Rhade find the refugees they were supposed to pick up from Seefra Five killed by their former general.
Harper has been captured by General Burma, a man who believes all technology to be evil. Dylan struggles with recovering Harper, evacuating all the remaining Seefran planets to Seefra One, a.k.a. Tarn-Vedra, and dealing with Trance. Dylan supposes that something may have happened to Trance while inside Methus-2, the artificial sun they fixed and the last place Trance seemed to be herself, and goes to investigate.
Dylan and his crew deal with the survivors on Seefra One promising them that it will soon become like Tarn-Vedra once was. Harper works on getting the "low-tech" mechanism inside the planet to work properly, while Trance explores her new powers resulting from the re-establishment of her sun. She introduces Dylan to the group that her impersonator worked for, "the Nebula," a group of stars controlling all the galaxies, also an enemy of the Abyss.
The Earth explodes before Harper makes his visit, the Andromeda manages to save Harper from destruction and runs from a Nietzschean attack fleet coming from the ruins of the planet. Analyzing fragments of the destroyed planet, Romy finds radical isotopes, proof that the Abyss aided the Nietzscheans in the destruction of Earth. Dylan consoles Harper for his loss, then prepares for the battle against the joined Nietzschean fleet, comprised of the Drago-Kazov, Mandau, and Sabra-Jaguar fleets.