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Over forty years have passed since the end of the Cylon War, contested between the humans of the Twelve Colonies and man's creation, the Cylons.
The Galactica, one of the original twelve battlestars, is scheduled to be decommissioned. As part of the ceremonies, Commander Adama's son Lee ("Apollo") is named to fly Adama's restored Viper. Lee's return opens old wounds when they discuss the fate of Adama's other son, Zak.
Meanwhile, in Caprica City, the famous scientist Gaius Baltar argues against limits on research into artificial intelligence. He also has a sensual new lover with a mysterious agenda of her own.
With all others in the line of succession dead, Laura Roslin, the Secretary of Education, is appointed President of the Twelve Colonies. She plans to gather up all the ships that survived the Cylon attack, including the Galactica, and flee the Colonial homeworlds, never to return.
Lee Adama, the new commander of the battlestar Pegasus, appoints the tough Lt. Kendra Shaw as his executive officer. Having served under the ruthless Admiral Cain, Lt. Shaw struggles with the lingering memories of those harsh times.
Major Shaw has a dangerous plan to rescue a missing Raptor crew from a mysterious enemy. Meanwhile, Lee Adama realizes that Shaw was involved in a controversial military operation under Admiral Cain's command.