The second war against the Cylons is over and The Twelve Colonies have been destroyed. Now Commander Adama of the Battlestar Galatica and President Laura Roslin lead a ragtag fleet of refugees in a supposed search for the fabled lost thirteenth colony, Earth. However, the dangers they face are many which compound an already difficult situation. In addition to the Cylons hunting and attacking the fleet in space and their infiltrator units carrying out sabotage-even as their former unwitting pawn, Gaius Baltar, helps in the hunt for them while hiding both his own guilt and the strange presence that haunts his every thought, the fleet also faces internal political conflict in which the rabble-rousing figure, Tom Zarek, is merely the loudest dissenting voice, not to mention recurring shortages of food, water and even oxygen. In the midst of these trials, however, clues begin to appear to suggest that Adama's bluff about finding Earth might hold more truthful than anyone could have guessed.

Humanity has reached for the stars and populated twelve planets as colonies of their home planet Kobol in a distant part of the galaxy. Scientific advancement has created robots with artificial intelligence, the Cylons, that rebel against humanity and after a war agree to go their own way. But, 50 years later, the Cylons return with 12 advanced models capable of appearing human and quickly dominate humanity wiping out most and forcing some 50,000 humans to flee in ragtag fleet through space. The Cylons are confident that they are superior to the humans supposedly lacking many emotional flaws and possessing an abliity to be reborn into new bodies with memories of their past lives as well as an ability to share memories with replicate models. However, Cylons are unable to reproduce and unable to communicate with their one god that they believe replaces the human belief in Gods, so they are keen to gain these abilities from their human creators. Unable to reproduce among themselves, they attempt to reproduce with humans and insist that reproduction can only be successful if the humans fall in love with them, which is challenging to accomplish in part because the Cylons cannot shut up about how superior they are to humans. The Cylons avoid wiping out the remaining 50,000 humans preferring to chase them back to Earth in hopes of forcing a meeting with their god. The humans initially allow the remaining military to lead their flight but eventually accept that they need to cooperate and put aside past colony specific prejudices in order to survive as a species as their populationo dwindles. Civilian leadership chooses to abandon the quest for Earth and settle on another planet where the Cylons find them and enslave them. This causes a rift among the advanced Cylon models and a rift among the humans forcing new alliances, a civil war among the Cylons and a continuation of the flight to Earth. When Earth is finally reached, it is surprisingly uninhabitable due to an ancient nuclear war. Out of hope, the humans despair but the one god sends angels to guide them to a new planet where the Cylons and humans can co-exist peacefully.