When Harper accidentally overrides Andromeda's personality with an older version, she hunts down the crew and goes on an old mission in which her former crew was slaughtered.

The crew of the Andromeda meet an alien race they were destined to face.

A Commonwealth conference becomes a backdrop for Magog espionage, while Harper tries to discover how one of their spies managed to remove some of his Magog larvae.

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.

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 crew encounter a POW camp full of captured High Guard starships and their AI avatars.

It's the start of the war between the Systems Commonwealth and the Nietzschean fleets. Captain Dylan Hunt and his ship the Andromeda Ascendant try to flee the first Nietzschean attack to warn the Commonwealth. In his attempt to escape, the Andromeda and Captain Hunt are caught in the event horizon of a black hole and frozen in time for 300 years. The crew of the Eureka Maru with Captain Beka Valentine try to salvage the Andromeda to sell for a Nightsider's ransom. After the Andromeda is pulled free, Hunt is unfrozen and forced to defend his ship against the salvagers and the Nietzschean mercenaries lead by Tyr Anasazi.

When the crew prepares for the launch of The Resolution of Hector, they soon discover that Rommie has had a change of mind and is now working against the crew. Knowing that this is not normal, Dylan sets out to reclaim the ship, and find out what is controlling his friend.

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

The Andromeda encounters the Arkology, a society that they believe is the closest to perfection humanity will ever achieve. But the Magog are close, and Dylan and the crew must convince the utopia that peace is not the answer. Conflict arises in the core crew when the leaders of Arkology do not wish to leave. Dylan wants to defend them, and Beka warns him that she's not going to stay and die defending an idea of peace.

The crew of Andromed encounter plague victims infected by a hostile, nanobot-based lifeform out to take over the ship.

The Andromeda crew search for a colony that disappeared.

The crew returns for the first time to Earth, where Harper and his cousin try to save the homeworld from Nietzschean occupation.

Andromeda encounters her damaged sister ship, the Pax Magellanic, that leads the crew of the Andromeda Ascendant on an eerie mission.

Tyr learns that he is a father.

As the Nietzschean fleet approaches, the Andromeda prepares for the final battle.

An arranged marriage between two rival Nietzschean Prides puts the Andromeda Ascendant in danger when Captain Dylan Hunt agrees to transport the bride to the wedding.

Dylan is faced with a difficult decision when Andromeda slipstreams back in time -- days before the climactic battle of the Nietzschean Revolution where the Commonwealth was defeated and the Nietzschean Alliance was destroyed.

Dylan and the crew search for a Nietzschean slip-scout carrying a probe that enables one to map every meter of the slipstream

Dylan and the crew of the Eureka Maru agree to join forces and become one team aboard the Andromeda Ascendant as they set forth on his mission to restore the Systems Commonwealth.

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.

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 a violent pride. Can Dylan find the culprit before the Maru is next?

Trance is held captive, while Dylan and the rest of the crew try to uncover the source behind mysterious attacks on cargo ships.

Dylan and Rhade receive a month-old distress signal from Beka. After following the coordinates she left, they find the Andromeda dead in space. On board, he finds Darregacorp engineers trying to salvage it, led by Jonah Derrega, and Beka Valentine.

The crew encounter the Vedrans the long-lost founders of the Commonwealth.

"Okay, that did not work," Trance says. "Let's try again." Trance tries to figure out how to help the crew survive a deadly intruder.

Harper finds himself overloaded with information when a dying Perseid transfers data into his brain.

A deadly enemy from the past returns with plans to create an elite warrior race.

A stranger gives Dylan a message from his dead fiancée leading him to an untouched world with descendants of his former crew and friends, including the descendant of his treachorous former best friend.

Rommie sets out to extract an informant, but winds up stuck on a planet with a strong hatred and fear of Androids.

In a race against Tyr to control the Route of Ages, the crew find themselves in another universe. To save them, Trance finally reveals who and what she really is.

Captain Dylan Hunt must save the Andromeda from the Nietzscheans, who are trying to persuade Tyr to help them destroy the ship and rebuild his Nietzschean life. His new life would include a wife to carry on his lineage.

Dylan and an old friend try to prevent the maker of the Magog Worldship from deploying an army of androids.

Dylan runs into a problem while analysing a black hole and imagines what his life would be like with a family before the common wealth fell.

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.

The avatar of the black hole, that trapped Dylan after the Nietzschean ambush, returns to get him back.

Dylan finds himself on Seefra-1, one of nine identical planets orbiting two suns. He soon encounters Rhade, who has abandoned all hope. Rhade hates Dylan for the hope he has brought, and when someone asks Dylan be killed, Rhade agrees to do it.

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.

The crew is tormented by a mysterious stranger who accuses them of murder.

After being repeatedly attacked by bounty hunters after several evasive slipstream jumps, Dylan determines that there must be a mole on board. After analyzing data recordings, he discovers that Beka has been infected by The Abyss and has unknowingly been giving away Andromeda's position. Dylan and the crew have to come up with a way to rid Beka of The Abyss -- without killing her.

The Andromeda picks up a group of refugees who have been subjected to psychological and physical torture.

After rescuing some people from a storm, a 'maggot' is brought onto Andromeda. This maggot chews through the systems and activations 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...

An explosion sends Dylan into an inter-dimensional loop, with a man named Elysian telling him to decipher a riddle.

As an old friend of Beka's has died, she tells the crew about her past.

Beka's Uncle Sid returns, as a candidate for a leader of the Commonwealth. He plans to use the Andromeda to help his chances, but an assassin has other plans for him.

Dylan is put on trial for high crimes against the Commonwealth.

The Andromeda is on the edge of a dimensional portal searching for Beka and Tyr, but when they return things may not be as they seem.

Dylan is taken captive and forced to admit that he killed the Mobius leader and overthrew the Mobius government more than 300 years ago.

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, Try 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?

Dylan receives a mysterious package, but is then framed for the murder of its sender so Dylan and Harper go on a mission to clear his name.

While the Andromeda is confronted by the Commonwealth fleet and Tri-Jema, Dylan must decide whether or not he can entrust the Route of Ages to them.

The Collectors have been using a drug to modify people's behavior, discovering their fears in efforts to control or break them. This is their solution for dealing with Dylan. Led by a message from Rev Bem, claiming to have a weapon that can defeat the oncoming darkness, Dylan lands on a drug-trafficking planet and is soon taken captive by the Collectors.

The unexpected return of Flavin takes Dylan on a journey through time, revealing mysteries surrounding Tarn Vedra, the Paradine, the battle with the Worldship, and Trance.

Tyr and Rommie are framed for the assassination of the Castalian president.

When a valuable painting gets stolen after Beka, Rhade, and everyone else in the bar inhales a mysterious mist, Dylan jumps at the opportunity to win the reward for reclaiming it so the Andromeda can be repaired. After tracing the nanobots in the mist, they encounter Harper who is accompanied by a beautiful woman named Doyle. But Harper is caught up in the plans of Marika, who wants him to genetically engineer Vedrans, as well as to take over the Seefra system.

A humanoid robot visits the Andromeda crew, helps them fight off a culture of organized machines and learns what it means to be a living being.

The crew travels to the core of Seefra's sun Methus-2 to repair it.

The crew searches for a princess abducted by a ruthless pirate. As usual, nothing is as it seems. Along the way, a secret from Beka's past is revealed.

The crew intercepts a mysterious cargo en route to a war zone.

Trance, Harper and their former employer Gerentex are unwilling partners on a wild ride to find a valuable artifact.

Dylan and Rhade attempt to infiltrate a mining camp where crystals are extracted, which contain the power needed to restore the Andromeda and leave the Seefra system.

Rev Bem gets a call from a Wayist friend in need of his help to save the Hajira and its settlement, Serendipity, from being taken over by slavers.

Dylan, Beka, Rev Bem and Tyr pursued by a gang of Neitzscheans, are forced to make a crash landing on an icy planet.

The arrival of Trance's sun threatens to destroy all the planets except Seefra-1 unless the system problem is fixed.

Hunting for the woman who set up the only major interstellar alliance since the Fall, Dylan finds himself in a bar at the edge of a desert wasteland, trying to fend of a Kalderan attack.

Dylan plays a dangerous game against two gamblers, but not everything is as real as it seems.