The Commonwealth spanned three galaxies and a myriad of cultures. Dylan Hunt, captain of the starship Andromeda, was frozen in time and awoke three centuries later to find the Commonweath 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. More and more worlds sign on, contributing their fleets to protect each other.
In the third season, Dylan and the crew travel from world to world as instructed by the Triumvirate, the leaders of the Commonwealth. But everything is building to the moment from one of his crew will betray him.
The fourth year deals with the corruption of the Commonwealth after the recent betrayal. Things become more intense as the Andromeda is expelled from the Commonwealth, Trance reveals her true form, Harper holds a weapon capable of destroying the Commonwealth, Beka becomes possessed by the Spirit of the Abyss, and a new crew member joins. But the Magog Worldship is nearing, and the final confrontation is to protect a Utopian society from it.