The start of the second series, with the conclusion to season one's cliffhanger! Dylan Hunt is the captain of the Andromeda Ascendant, a ship which serves in the military force of the Systems Commonwealth, a monarchy which spans several galaxies. Hunt and his ship are subsequently frozen for several centuries. Revived by a passing salvage ship, Hunt is horrified to find that the Commonwealth has collapsed and all known galaxies have descended into barbarism. Hunt decides to take his ship and crew on a trip around the cosmos to attempt to restore order to the known galaxies.

The Widening Gyre
After being attacked by the massive Magog Worldship, the Andromeda Ascendant drifts heavily damaged in space, with most of the crew injured and unconscious. As the Magog begin a shipboard attack on the survivors, Dylan and Rommie launch a desperate rescue mission into the heart of the Worldship, where Harper discovers he is infested with Magog eggs.

Exit Strategies
The Eureka Maru crashes on an icy planet when it is attacked by Nietzcheans, leaving Dylan, Tyr, Beka and Rev Bem stranded. While trying to devise a way to repair the ship, they discover a vicious genetically engineered life-form that lives under the planet's surface. Meanwhile on Andromeda, Harper is still disturbed by the recent Magog attack.