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.