USS Yorktown, now with large torpedo holes on both sides amidships, floated through the night of 6-7 June 1942, while her escorting destroyers unsuccessfully pursued the Japanese submarine I-168, treated injured sailors and kept watch. As dawn approached, it was clear that the carrier was lower in the water with an increasing list. As the sun rose on 7 June, Yorktown rolled over on her port side and sank by the stern.

She was not seen again by human eyes until 19 May 1998, when an expedition led by Dr. Robert Ballard located and photographed her wreck, sitting upright on the sea floor with a 25-degree list to starboard. Despite fifty-six years under 16,650 feet of salt water, Yorktown was in surprisingly good condition, with all but a little of her structure undistorted and readily recognizable. Measure 12 camouflage paint was still intact, and the white hull number "5" could be seen at her bow and stern. Evidence of Battle of Midway damage and the subsequent salvage efforts was abundant: the bomb hole in her flight deck aft of the midships elevator; fire-damaged paint and metal on her smokestack; a huge torpedo hole in her port side; anti-aircraft guns still pointing skyward and other guns missing where they had been jettisoned by the salvage party on 6 June 1942.