The discovery of the ship’s remains required detective work to get a more accurate location for the Indianapolis when it was struck with two torpedoes from the Japanese submarine.

A naval historian, Richard Hulver, came across a blog post that led him last year to a ship’s log recording a sighting of the Indianapolis. Calculations using that record showed that the cruiser was west of where it had long been assumed to be. Using a ship equipped with advanced undersea search equipment, Mr. Allen’s team began combing the newly identified area.

Mr. Allen, whose father fought in World War II, has made a passion of finding and preserving artifacts from the war. His expedition said that the precise location of the Indianapolis would be kept secret from the public, and that the site would be respected as a grave, as American law requires.

Just before the Indianapolis sank, it had completed a top secret mission: shipping parts of the atomic bomb, code-named “Little Boy,” that was later dropped on Hiroshima from San Francisco to Tinian Island in the Western Pacific. Allied forces were closing in on Japan, and the Indianapolis was ordered to sail to Leyte in the Philippines to get ready for the assault.

But as the Indianapolis plowed on in the dark of night, a Japanese submarine spotted it, and just after midnight unleashed six torpedoes, two of which struck the American cruiser. The explosions knocked out the ship’s communications, and the order to abandon ship came only by word of mouth. The ship sank in minutes.

For the 800 or so sailors and Marines who made it overboard, another, longer ordeal waited. They plunged into water covered in fuel oil, and many soon began vomiting. They had 12 or so rafts and few supplies, and it was unclear whether the distress messages had gone out before the communications system failed.