Auxiliary fire control
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Located in the forward section of battlestar Galactica is Auxiliary Fire Control. This area likely allows the battlestar's gun batteries or missile launchers to be fired in the event that CIC cannot control these functions or if the command crew is incapacitated.
Cylon Centurion forces that board battlestars typically use a strategy where their boarding parties take control of Auxiliary Fire Control as well as Aft Damage Control. The Cylons in Aft Damage Control (which can controls bulkheads and vents throughout the ship) will attempt to vent the ship's atmosphere into space, asphyxiating the crew so that the Cylons have full control of the battlestar. From Auxiliary Fire Control, the Cylons would then turn a battlestar's gun batteries at other Colonial ships to destroy them.
Colonel Saul Tigh recalls this tactic while Galactica is boarded by advanced Centurion models after they escape from a basestar and its attacking force (Scattered). Tigh learns of this ploy from William Adama, as he recalled a similar attempt by Cylons that invaded Galactica while he was stationed there in the last week of the Cylon War some 40 years earlier.
To combat the Cylons, Tigh (in command of Galactica after Commander Adama is shot by a Cylon agent) orders teams to stop the boarders from reaching these key control areas (portions from deleted scene, "Valley of Darkness").