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.

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.

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 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.

Finally, after 300 years and a black hole keeping them apart, Captain Dylan Hunt reunites with his true love, Sara.

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 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.

Tyr learns that he is a father.

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

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.

With their communication with the crew of the Eureka Maru completely cut off, Dylan and Rommie are forced into exile on a prison planet and must befriend fellow inmates to attempt any escape.

A crash landing on a strange planet leaves Tyr with a complete loss of memory and a mystery crate to protect from not-so-brotherly Nietzcheans.

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

Rommie falls in love with a surviving android (Michael Shanks) of a destroyed ship, only to be betrayed as he turns out to be the ultimate enemy.

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.

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.

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.

Teen royalty is the key to the crew quelling an alien uprising, as Dylan and Tyr become co-regents to a recently orphaned young prince.

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

Dylan hijacks a starship to lose the Ogami.

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

Beka, Dylan and Trance attempt to find the Engine of Creation, an artifact able to rearrange space and time.

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

The Andromeda is swallowed by a space creature.