By May 28, the Navy knew the submarine had been destroyed. The SOSUS underwater surveillance system, designed to detect Soviet submarines, had heard it explode underwater. Scorpion’s remains would later be found by deep-diving submersibles under two miles of water, in a debris field 3,000 by 1,800 feet.

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.

(This first appeared several years ago.)

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.

The Skipjacks were smaller than nuclear submarines today, with a displacement of 3,075 tons and measuring just 252-feet long by 31-feet wide. They had a crew of ninety-nine, including twelve officers and eighty-seven enlisted men. The class was the first to use the Westinghouse S5W nuclear reactor, which gave the submarine a top speed of fifteen knots surfaced and thirty-three knots submerged.

The primary armament for the Skipjack class was the Mk-37 homing torpedo. The Mk-37 had an active homing sonar, a range of ten thousand yards with a speed of twenty-six knots, and a warhead packed with 330 pounds of HBX-3 explosive.

Scorpion was only eight years old at the time of its loss, relatively new by modern standards. Still, complaints from the crew that the sub was already showing its age were rampant. According to a 1998 article in the U.S. Naval Institute Proceedings, Scorpion had 109 unfulfilled work orders during its last deployment. It had “chronic problems” with its hydraulics, its emergency blow system didn’t work and emergency seawater shutoff valves had not yet been decentralized. At the start of its final patrol, 1,500 gallons of oil leaked from its conning tower as it left Hampton Roads.

Two months before its loss, Scorpion’s captain, Cdr. Francis Atwood Slattery, had drafted an emergency work request for the hull, which he claimed “was in a very poor state of preservation.” He also expressed concern about leaking valves that caused the submarine to be restricted to a dive depth of just three hundred feet—less than half of the Skipjack’s test depth. Many had taken to calling the submarine the USS Scrapiron.

On May 20, the commander of the Navy’s Atlantic submarine fleet had ordered Scorpion to observe a Soviet flotilla in the vicinity of the Canary Islands. The Soviet task force, which consisted of an Echo-II-class submarine, a submarine rescue vessel, two hydrographic survey ships, a destroyer and an oiler were thought to be taking acoustic measurements of NATO surface ships and submarines.

On May 21 Scorpion checked in by radio, noting its position and estimating its return to Norfolk on May 27. The report noted nothing unusual.

By May 28, the Navy knew the submarine had been destroyed. The SOSUS underwater surveillance system, designed to detect Soviet submarines, had heard it explode underwater. Scorpion’s remains would later be found by deep-diving submersibles under two miles of water, in a debris field 3,000 by 1,800 feet.

What happened to Scorpion? The U.S. Navy’s report on the incident is inconclusive. A number of theories—and at least one conspiracy have arisen to explain the loss of the ship and ninety-nine crew members, but all lack hard evidence.

One theory advanced by a technical advisory group convened by the Navy to examine the physical evidence is that the Scorpion had fallen victim to a “hot-run” torpedo, a torpedo that accidentally becomes active in the tube. Unlike other gas-ejected torpedoes, the Mk-37 swam out of the tube, a quieter egress that prevented submarine detection. This theory is bolstered by reports that the submarine was headed in the opposite direction at the time of destruction as was anticipated—a common solution for a hot-run torpedo was to turn 180 degrees to activate its anti-friendly-fire failsafe, which prevented it from turning on the firer.

Another theory is that the Trash Disposal Unit (TDU) had experienced a malfunction that flooded the submarine, spilling seawater on its sixty-nine-ton battery and causing it to explode. The Scorpion had in fact been awaiting a new TDU latch, and the system had caused the submarine to flood in the past.

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.

The conspiracy theory is that the Scorpion was somehow caught up in some kind of Cold War skirmish, and that the Soviet flotilla had sunk the sub. An unusually high number of submarines were sunk in 1968, including the Israeli submarine Dakar, the French submarine Minerve, and the Soviet submarine K-129. According to conspiracy theorists, the Cold War had briefly turned hot under the waves, leading to the loss of several submarines. Unfortunately, there is no actual proof, nor an explanation for why a Soviet task force with only two combatants could manage to kill the relatively advanced Scorpion.

There will likely never be a conclusive explanation for the loss of USS Scorpion. While disconcerting, the U.S. Navy has not lost a submarine since. The loss of Thresher and Scorpion and their 228 crew were hard lessons for the Navy to absorb, but absorb them it did. Tens of thousands of submariners ultimately benefitted—and returned safely home.

Kyle Mizokami is a defense and national-security writer based in San Francisco who has appeared in the Diplomat, Foreign Policy, War is Boring and the Daily Beast. In 2009 he cofounded the defense and security blog Japan Security Watch. You can follow him on Twitter: @KyleMizokami.