So what happpenned?
A final theory is that the Scorpion experienced a hydrogen explosion during or immediately after charging its batteries. At the time of the explosion, the submarine was at periscope depth and likely at “Condition Baker”—the closing of watertight hatches. An anachronistic holdover from the non-nuclear days, the closing of hatches could have caused a buildup of explosive hydrogen in the battery area, a process that occurred during battery charging. A single spark from the batteries could have caused a hydrogen gas explosion that then led to a battery explosion. This correlates with two small explosions aboard the submarine that were picked up by hydrophones a half-second apart.
In May 1968, a U.S. nuclear-powered attack submarine was sent on a secret mission to spy on the Soviet navy. Seven days later, with the families of the crew waiting dockside for the USS Scorpion to return from a three-month patrol, the U.S. Navy realized that the submarine was missing. Scorpion had been the victim of a mysterious accident, the nature of which is debated to this day.
The USS Scorpion was a Skipjack-class nuclear attack submarine. It was one of the first American submarines with a teardrop-shaped hull, as opposed to the blockier hull of World War II submarines and their descendants. It was laid down in August 1958 and commissioned into service in July 1960.