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On 23rd century Constitution class starships the guidance system was also known as guidance computers. In 2269, when the USS Enterprise was in orbit around the Shore Leave Planet the ship malfunctioned and Chief Engineer Lieutenant Commander Montgomery Scott was in temporary command he requested from Lieutenant M'Ress a print-out of the ship's guidance computer's last orders. In reviewing the orders, M'Ress noticed that something was very strange, and the only reason why the new orders from Scott were not being carried out was because navigator Lieutenant Arex had had all the engine controls manually locked. But as would soon be learned this wasn't the fault of Arex, but instead the fault of the planet's master computer that was suffering from it's version of a mental breakdown. (TAS: "Once Upon a Planet")
Doctor Timicin of Kaelon II modified the guidance system of Starfleet photon torpedoes. Those modified torpedoes would enable him to implement his theory of helium fusion enhancement and possibly revitalize the Kaelon sun. (TNG: "Half a Life")
In early 2373, Captain Benjamin Sisko theorized that a possible reason for the Vorta commander Kilana's interest in a downed Jem'Hadar attack ship was that she wanted to recover its guidance system. (DS9: "The Ship")
The guidance system of the same Dominion ship, used by Captain Sisko and his crew to destroy a Dominion ketracel-white facility in 2374, was damaged during the facility's destruction. (DS9: "A Time to Stand")