After forty years of armistice, the Cylons attack the Twelve Colonies of Kobol. Their strategy: a virus implanted into mankind's defense system. The former Battlestar Galactica, which is being adapted into a museum, is not connected with the defense system and becomes the only warship capable of fighting against the Cylons in the hopes of leading the survivors to planet 'Earth'.

In a distant part of the galaxy lie The Twelve Colonies of Man, a civilization that has been at peace for some forty years with an empire of machines, the Cylons, who were created generations before as worker drones for mankind, but became independent, rose in rebellion, and launched war on their masters. Now, the Cylons have evolved into more human form, into machine-created biological beings, who seek to exterminate true biological humans. To this end they use a human scientist, Gaius, to help one of their infiltrators, known as #6, penetrate the Colonies' master ...