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.

Beka's con-artist brother unexpectedly shows up claiming to be a devout Wayist making the Andromeda a prime target for Restorian attack.

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

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.

Beka Valentine receives a distress call from her beloved Uncle Sid , but to her disdain realizes that he has become Sam Profit, a big business tycoon.

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.

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.

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.

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.

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

The Andromeda is swallowed by a space creature.

Tyr learns that he is a father.