The governing body of the Commonwealth has voted "no-confidence" in triumvir Tri-Jema, she sends Dylan to get the Andromeda refitted and visit an augur, who is told to be infallible. This augur, dubbed Citizen Eight, aims to take Tri-Jema's place as triumvir and, according to the triumvir, remove Dylan from command of the Andromeda. The robots sent to the Andromeda to start pre-upgrade repairs turn against the crew, forcing Dylan and Harper to shut them down. Dylan must deal with Citizen Eight before he can bring down the Commonwealth from within.
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.