The Colonies' survivors have found their hopes of eluding their Cylon pursuers dashed by an invasion and occupation of their new home. As the fate of all human life hangs in the balance, friends become enemies, enemies become unexpected allies, and decisions are made that will haunt some people for the rest of their lives.

When the crew of the Enterprise is called back home, they find that an unstoppable force of terror from within their own organization has detonated the fleet and everything it stands for, leaving the world in a state of crisis. With a personal score to settle, Captain Kirk leads a manhunt to a war-zone world to capture a one-man weapon of mass destruction.