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.

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.

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

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

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

Tyr learns that he is a father.

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.

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.

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

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.

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.

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?

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.

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

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

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

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

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?

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.

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.

The Andromeda is swallowed by a space creature.

Gaheris Rhade sets out to reshape the universe according to his will and restore order amid the chaos

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....

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.