The Andromeda encounter 2 ships with depleted engines and weapons. They come from a planet, where the two sides have been fighting for as long as anyone can remember. One side is suffering from a disease, they claim the other side is using biological weapons, but the other side says they didn't do it. When Dylan becomes infected, the crew must figure out the source of the virus to save the captain.
The Commonwealth spanned three galaxies and a myriad of cultures. Dylan Hunt, captain of the star ship Andromeda, was frozen in time and awoke three centuries later to find the Commonwealth had fallen.
To fight back the chaos among the stars, Hunt must use the Andromeda to restore the Commonwealth and bring unity to the galaxy once again. He recruits a mercenary, Tyr Anasazi, and the crew of the Eureka Maru: Captain Beka Valentine, Engineer Seamus Harper, Physicist Rev Bem, and Medical Officer Trance Gemini.
After discovering the Spirit of the Abyss and its powerful weapon, the Magog Worldship, the need for the Commonwealth is greater than ever. 50 member worlds are finally recruited, and the reconstruction of the Commonwealth is finally truly underway.