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(covers information from several alternate timelines)
The mirror universe counterpart of Jonathan Archer utilized auto-navigation to lock the Imperial Flagship ISS Enterprise on a course for the Vintaak system in order to investigate the recovery by the Tholians of a mysterious Earth vessel from a parallel universe. Archer encrypted the controls with a random code, making it impossible to release auto-navigation before Enterprise reached its destination. (ENT: "In a Mirror, Darkly")
In an alternate reality, Captain Richard Robau of the USS Kelvin ordered Lieutenant George Kirk to use the auto pilot and set a collision course with the Narada after the Kelvin was critically damaged in battle. The auto pilot experienced a malfunction following another attack by the Narada, forcing now-acting captain George Kirk to manually fly the Kelvin into the Narada while he remained on board in order to allow the fleeing shuttlecraft to escape. (Star Trek)
While on their way back to the USS Enterprise-D in 2369, Data activated the automatic helm control of the runabout and joined the fellow officers in the aft section of the ship. The computer voice verified this order. (TNG: "Timescape")
In an alternate 2373, Yedrin Dax supplied the crew of the USS Defiant with the navigation logs from a crash that had stranded the ship on a planet in the Gamma Quadrant. Yedrin instructed Jadzia Dax to download the logs into Defiant's auto-pilot in order to recreate the accident. (DS9: "Children of Time")
While attempting to move the USS Equinox away from the USS Voyager when its warp core was about to explode, Kathryn Janeway urged Ransom to set auto-navigation and beam aboard her ship. Ransom refused, claiming there was no time, and perished in the explosion. (VOY: "Equinox, Part II")