For an unusually long period of time, beginning shortly before midnight on 20 May and ending after midnight 21 May, Scorpion attempted to send radio traffic to Naval Station Rota, but was only able to reach a Navy communications station in Nea Makri, Greece, which forwarded Scorpion's messages to ComSubLant.[10] Lt John Roberts was handed Commander Slattery's last message, that he was closing on the Soviet submarine and research group, running at a steady 15 knots at 350 feet "to begin surveillance of the Soviets".[11] Six days later the media reported she was overdue at Norfolk.[12]
The Navy suspected possible failure and launched a public search. Scorpion and her crew were declared "presumed lost" on 5 June. Her name was struck from the Naval Vessel Register on 30 June. The public search continued with a team of mathematical consultants led by Dr. John Piña Craven, the Chief Scientist of the U.S. Navy's Special Projects Division. They employed the methods of Bayesian search theory, initially developed during the search for a hydrogen bomb lost off the coast of Palomares, Spain, in January 1966 in thePalomares B-52 crash.
Some reports indicate that a large and secret search was launched three days before Scorpion was expected back from patrol. This, combined with other declassified information, leads to speculation that the U.S. Navy knew of the Scorpion's destruction before the public search was launched.[13]
At the end of October 1968, the Navy's oceanographic research ship, Mizar, located sections of the hull of Scorpion on the seabed, about 740 km (400 nmi; 460 mi) southwest of the Azores,[14] under more than 3,000 m (9,800 ft) of water. This was after the Navy had released sound tapes from its underwater "SOSUS" listening system, which contained the sounds of the destruction of Scorpion. The court of inquiry was subsequently reconvened and other vessels, including the bathyscaphe Trieste II, were dispatched to the scene, collecting many pictures and other data.
Although Craven received much credit for locating the wreckage of Scorpion, Gordon Hamilton, an acoustics expert who pioneered the use of hydroacoustics to pinpoint Polaris missile splashdown locations, was instrumental in defining a compact "search box" wherein the wreck was ultimately found. Hamilton had established a listening station in the Canary Islands that obtained a clear signal of what some scientists believe was the noise of the vessel's pressure hull imploding as she passed crush depth. A Naval Research Laboratory scientist named Chester "Buck" Buchanan, using a towed camera sled of his own design aboard Mizar, finally located Scorpion.[14] The towed camera sled, which was fabricated by J. L. "Jac" Hamm of Naval Research Laboratory's Engineering Services Division, is housed in the National Museum of the United States Navy. Buchanan had located the wrecked hull of Thresher in 1964 using this technique.