Command and control systems
The command and control systems were systems key to maintaining the propulsion systems aboard a starship. Aboard Intrepid-class and Defiant-class starships, command and control was located in main engineering. (VOY: "Deadlock")
When the USS Defiant temporarily captured by the Dominion in 2374, Captain Benjamin Sisko was ordered by his Jem'Hadar captor Kudak'Etan to repair the ship's damaged warp drive. When Sisko explained that he couldn't do the job alone and that he would need some of his crew, otherwise, if he were to utilize the assistance of his captors, he would first need to train them on the ship's primary command and control systems– which require six hours alone– before they could "move up to basic engineering theory for a class 7 warp drive." Given this information, the Jem'Hadar relented and allowed Sisko to take three bridge officers with him to assist in the repairs.
Later, after Kira Nerys trained her Jem'Hadar assistant in her task of reconnecting the deuterium injector by showing him to slowly power up the plasma relay, in an attempt to stall the repairs to the warp drive, she yelled to him that he was powering it up "too fast" and told him to "reinitialize the system and start again, but do it at about half the speed this time." She then told Sisko, as an aside, that "he's not stupid," and that he deception will only work for so long, because "he's already got the entire command and control system committed to memory." (DS9: "One Little Ship")
After the USS Protostar's nacelles became entangled in vines from the planet it had set down on, and the cilia from the superorganism that was holding the ship began to infiltrate the ship's ventral superstructure, Hologram Janeway noted that due to these series of evens, the ship's command and control functions were offline. (PRO: "Dream Catcher")