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The nuclear-powered submarine Scorpion got the top-secret message shortly before midnight: Change course and head for the Canary Islands, where a mysterious collection of Soviet ships had caught the Navy’s eye.

It was May 17, 1968, and a visit to the U.S. sub base in Rota, Spain, was the last time anyone saw the Scorpion. The submarine sank five days later.

About five months later, the Scorpion’s wreckage was found on the ocean floor, two miles deep in the Atlantic, along with the bodies of 99 crewmen.

For decades, the Navy has said the Scorpion sank because of a mechanical malfunction while returning from the Mediterranean to its home port of Norfolk, Va.

Navy spokesman Frank Thorp said Tuesday the Navy had established several possible scenarios for the loss of the sub but still is “unable to make a conclusive determination regarding the cause of the loss.”

In fact, however, the USS Scorpion at the time it sank was at the center of a web of espionage, high-tech surveillance and a possible Cold War military clash that resulted in an alleged agreement by the U.S. and the Soviet Union to cover up the full accounting of what happened.

A review of hundreds of documents and interviews with dozens of current and former military personnel presents a scenario dramatically different from the Navy’s official version:

– The Scorpion was not on a routine crossing of the Atlantic, but had been diverted to a top-secret mission to spy on a group of Soviet ships, including a nuclear submarine.

– Although the Navy’s official explanation was of a mechanical malfunction, that countermanded an earlier conclusion by a panel of senior Navy officials that the vessel was sunk by a torpedo. The panel concluded it was one of the Scorpion’s own torpedoes, gone awry.

In late 1993, the Navy declassified most of the court’s conclusions. Headed by retired Vice Adm. Bernard Austin, the Scorpion court concluded that the best evidence pointed to an errant Scorpion torpedo that circled around and exploded against the hull of the sub.

The court’s conclusion stemmed in part from records showing the Scorpion had had a similar experience in 1967 with an unarmed training torpedo that suddenly started up and had to be jettisoned.

In 1970, a different Navy panel completed another classified report that disavowed the Court of Inquiry’s conclusion. Instead of an accidental torpedo strike, the new group suggested a mechanical failure caused an irreparable leak that flooded the submarine.

– The Scorpion believed it was operating in secret, but John Walker, the Navy’s most notorious spy, had given the Soviets the codes they needed to track the U.S. sub in the hours before it sank. The Soviets had the ability to monitor all electronic transmissions to the Scorpion, including the encrypted orders sending it on its spy mission.

– Several Russian admirals say senior Navy officials in both the United States and the Soviet Union agreed to never disclose details of the Scorpion incident and the loss of a Soviet missile sub in the Pacific two months earlier in 1968. To do so, they say, could have seriously damaged U.S.-Soviet relations.

A senior admiral in the Pentagon at the time of the Scorpion sinking said in a recent interview that U.S. intelligence agencies feared the submarine was headed into possible danger, based on intercepted Soviet naval communications in the Atlantic.

“There was some communications analysis . . . that the Scorpion had been detected by the group she had been shadowing and conceivably they had trailed her,” said retired Vice Adm. Philip Beshany. “There were some speculations that not only did they track her but attacked her.”

There is evidence that indirectly supports Beshany’s assertion that the U.S. intelligence community learned of a possible confrontation between the Scorpion and the Soviet warships it had been sent to spy on.

The Navy mounted a secret search for the submarine within 24 hours of its sinking, several retired admirals said. The search was so highly classified that the rest of the Navy, and even a Navy Court of Inquiry that investigated the sinking later in 1968, were never told about it.

The crew’s friends and relatives were told nothing; they assumed the sub was on its way home.