The Auxiliary Control Center was a key section aboard Constitution-class starships, that acted as a supplemental control center to the bridge and main engineering. If necessary, a starship could be controlled from this room alone.
Later that year, the USS Constellation was attacked by a doomsday machine dubbed the "planet killer". The ship was heavily damaged, with the main bridge being rendered uninhabitable. Commodore Matthew Decker beamed his crew down to the surface of the third planet in the star system L-374. Before he could beam down himself, another attack took the transporters off line, and Decker watched in horror as the Planet Killer destroyed the third planet and consumed the remains for fuel. When the Enterprise arrived, Decker was found in Auxiliary Control, suffering from severe shock. After beaming Doctor Leonard McCoy and Commodore Decker back to the Enterprise, Captain Kirk was able to command the Constellation from Auxiliary Control, eventually destroying the "planet killer" that threatened billions of lives in Federation space. (TOS: "The Doomsday Machine")
The malevolent Gorgan was able to gain temporary control of the Enterprise. Members of the engineering staff, including Lieutenant Commander Montgomery Scott, were led to believe that Captain Kirk's efforts to bypass the main bridge controls would result in the destruction of the ship. (TOS: "And the Children Shall Lead")
In 2269, the Auxiliary Control room of the USS Enterprise was commandeered by Dr. Sevrin and his followers in a successful bid to gain control of the ship in order to find what they believed to be the location of the planet Eden. (TOS: "The Way to Eden")
Defiant-class starships also contained an auxiliary control section. In 2374, when the USS Defiant lost phaser control while under attack by a Jem'Hadar ship, Captain Sisko ordered Commander Worf to Auxiliary Control in order to target the phasers manually. (DS9: "One Little Ship")