The episode opens with Beka, dead on the floor of Command. She has a hole in her chest. Harper's body is propped against a machine, being electrocuted. Tyr lies on the floor of a deck, also dead. Dylan is leaning against some bars, bleeding. In Slipstream Control, Rommie is picked up by a large stranger in black armor, and thrown down to the Core. The stranger activates an overload, and the Andromeda splits in two, then explodes. Trance, in a mysterious blue space, watches in horror. She is with one of her Bonzai trees. "Okay, that did not work". she says, "Let's try again".
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.