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.

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.

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.