The Annihilators are a rogue Cylon suicide cell dedicated to hitting random Colonial targets.
During the Cylon War, the Cylons programmed this force of Centurions without the ability to be recalled, and therefore are unable to desist hostilities despite the Armistice. The Colonials are only told of the Annihilators as part of the Armistice itself. After the end of the war, Galactica and a small task force are assigned to eliminate any remaining Annihilator cells (Battlestar Galactica: Origins 5).
En route to a known Annihilator stronghold, codenamed Trinity Base, a force of Annihilators jumps on top of Galactica and is able to board the ship before the Colonials are able to intercept the Heavy Raider. This force of Annihilators boards Galactica and is able to decompress the ship, killing many of Galactica's crew. However, a force lead by Captain Alexa Cain and Lieutenant William Adama are able to take out the Annihilators that commanded Aft Damage Control—although a Centurion thought destroyed kills Cain in the process (Battlestar Galactica: Origins 6).