With Norfolk her home port for the remainder of her career, Scorpion specialized in the development of nuclear submarine warfare tactics. Varying her role from hunter to hunted, she participated in exercises which ranged along the Atlantic coast and in the Bermuda and Puerto Rico operating areas; then, from June 1963 to May 1964, she interrupted her operations for an overhaul at Charleston, South Carolina. Resuming duty off the eastern seaboard in late spring, she again interrupted that duty from 4 August to 8 October to make a transatlantic patrol. In the spring of 1965, she conducted a similar patrol in European waters.
During the late winter and early spring of 1966, and again in the autumn, she was deployed for special operations. Following the completion of those assignments, her commanding officer received the Navy Commendation Medal for outstanding leadership, foresight, and professional skill. Other Scorpion officers and crewmen were cited for meritorious achievement. The Scorpion is reputed to have entered an inland Russian sea during a "Northern Run" in 1966 where it successfully filmed a Soviet missile launch through its periscope before being forced to use its high speed to flee Soviet Navy ships. Scorpion had a reputation for excellence and as a fast attack submarine it was a plum assignment for officers seeking to move up in a Navy in which submarine officers were gaining increasing clout.
As Scorpion's original "full overhaul" was whittled down in scope, it was decided it would not receive long-overdue SUBSAFE work. Scorpion would not receive a new, central valve control system; in the event of an emergency, her crew would have to scramble around the engine room to find and manually operate large valves. Crucially, Scorpion would not receive a fix for the same emergency system that did not work on the Thresher, the submarine whose loss was the reason for the existence of the SUBSAFE program. On that ship a pipe leak at depth prompted an emergency shutdown of the submarine's nuclear reactor; powerless, the Thresher could still have surfaced if the Emergency Main Ballast Tank blow system worked. It did not. (Later, dockside tests on Thresher's sister ship Tinosa proved that the EMBT system did not work at test depth; moisture in the high-pressure air flasks froze the valves shut.) Following a dispute between Charleston Naval Ship Yard, which claimed the EMBT system worked as-is, and SUBLANT, which claimed it did not, the EMBT was "tagged out" or listed as unusable. The aforementioned problems with overhaul duration, that saw the Scorpion selected for a reduced experimental overhaul program, also caused all SUBSAFE work to be delayed as well during 1967.
The reduced overhaul concept Scorpion went through had been approved by the Chief of Naval Operations on 17 June 1966. On 20 July, the CNO also allowed deferral of the SUBSAFE extensions, which had otherwise been deemed essential since 1963.
During Scorpion's last six months of operational life, at least two sailors, EM2 Daniel Rogers and Radioman Chief Daniel Pettey, struggled to be released from duty aboard Scorpion due to the bad morale problems they witnessed. Rogers sought disqualification from submarine duty - which was then allowed - while Pettey actually attempted to transfer to the U.S. Army only to be released from Scorpion while in the Mediterranean just months before it was lost.
Upon departing the Mediterranean on May 16, two men departed Scorpion at Rota, Spain. One man left due to emergency leave and the other enlisted man departed for health reasons. Scorpion was then detailed to observe Soviet naval activities in the Atlantic in the vicinity of the Azores. With this completed, Scorpion prepared to head back to Naval Base Norfolk.
For an unusually long period of time, beginning shortly before midnight on May 20 and ending after midnight May 21, Scorpion was attempting to send radio traffic to Naval Station Rota in Spain but was only able to reach a Navy communications station in Nea Makri, Greece, which forwarded Scorpion's messages to SUBLANT. Six days later, she was reported overdue at Norfolk. Navy personnel suspected possible failure and launched a search.
A public search was initiated, but without immediate success and on June 5, Scorpion and her crew were declared "presumed lost." Her name was struck from the Naval Vessel Register on June 30. Some recent reports now indicate that a large and secret search was launched 3 days before Scorpion was expected back from patrol; this combined with other declassified information led many to speculate the US Navy knew of the Scorpion's destruction before the public search was launched.
The public search continued, a team of mathematical consultants led by Dr. John Craven, the Chief Scientist of the U.S. Navy's Special Projects Division, employing the novel 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 the Palomares hydrogen bombs incident. At the end of October, the Navy's oceanographic research ship, USNS Mizar (T-AGOR-11), located sections of the hull of Scorpion in more than 3000 meters (10,000 feet) of water about 740 kilometers (400 nautical miles) southwest of the Azores. This was after the navy had released sound tapes from its underwater "Sosus" listening system which contained the sounds of the destruction of Scorpion. Subsequently, the Court of Inquiry was reconvened, and other vessels, including the bathyscaphe Trieste, were dispatched to the scene, collecting myriad pictures and other data.
Although Dr. Craven has received much credit for locating Scorpion's wreckage, Gordon Hamilton - an acoustics expert who pioneered the use of hydroacoustics to pinpoint Polaris missile splashdown locations - was instrumental, not only in acquiring the acoustic signals that were used in locating her, but also in analyzing those signals to provide a concise "search box", wherein the wreck of the Scorpion was finally located. Hamilton had established a quasi-legal listening station in the Canary Islands, which obtained a clear signal of what some scientists believe was the noise of her pressure hull imploding as she passed below crush depth. A little-known Naval Research Laboratory scientist named Chester "Buck" Buchanan, using a towed camera sled of his own design aboard the USNS Mizar, finally located Scorpion after nearly six months of searching. The towed camera sled, which was fabricated by J.L. "Jac" Hamm of Naval Research Laboratory's Engineering Services Division, is currently housed in the Navy Museum, Washington Navy Yard, Washington, DC. (Buchanan had located the wrecked hull of the USS Thresher in 1964 using this same technique.)
The aft section appeared to have skidded sideways on impact, since it was less hydrodynamically-shaped — unlike the bullet-shaped torpedo room, which investigators believed would have developed a greater downward velocity. The aft section of the engine room had telescoped forward into the larger-diameter hull section.
The only damage to the torpedo room compartment appears to be a hatch missing from the forward escape trunk; Palermo pointed out that this would have occurred when water pressure entered the torpedo room at the moment of implosion. He also pointed out that the aft escape trunk hatch is sprung open and appears twisted, though it is still on its hinges. (This conclusion was drawn by Palermo eighteen years after the Scorpion was lost when he reviewed new and extremely clear images taken by Jason Junior and Alvin as part of a Navy-Woods Hole Oceanogaphic Institute survey of the Scorpion's wreck site.)
Palermo could not rule out sabotage or collision as "plausible" causes of Scorpion's destruction. Palermo writes that the position of the masts and other evidence possibly indicate Scorpion was near the surface "just prior to sinking." Palermo admits that a precursor signal that occurred some 22 minutes prior to the acoustic train left by Scorpion's sinking "could have been the results of an internal explosion." Palermo states that "some of the remaining 14 acoustic events do have some of the characteristics of explosions", though he qualifies this by writing that such characteristics "may" also be attributed to other sources.
The 1970 Naval Ordnance "Letter", the intensive acoustics study of the Scorpion destruction sounds by Price and Christian, was a supporting study within the SAG report. In its Conclusions and Recommendations section, the NOL acoustic study states:
The Naval Ordnance Laboratory based much of its findings on an extensive acoustic analysis of the torpedoing and sinking of the USS Sterlet in the Pacific in early 1969, seeking to compare its acoustic signals to those generated by Scorpion. Price, a critic of Craven and Hamilton's analysis of the sounds emitted by the Scorpion, found the Navy's scheduled sinking of Sterlet fortuitous. It is problematic, however, that the Sterlet, a small World War 2 era diesel-electric submarine, was of a vastly different design and construction from Scorpion with regard to its pressure hull and other characteristics. Its sinking resulted in three identifiable acoustic signals as compared to Scorpion's fifteen, something Price could not adequately explain. The mathematical calculations Price used to arrive at his analysis – and dispute some of Craven and Hamilton's conclusions – remain unknown to the public.
When completed, the NOL acoustics study of the Sterlet and Scorpion sinking sounds provided a highly debated explanation as to how Scorpion may have reached its crush depth by anecdotally referring to the uncontrolled and nearly-fatal dive of the diesel submarine USS Chopper in January 1969:
In the same May, 2003 N77 letter excerpted above (see 1. with regard to the Navy's view of a forward explosion), however, the following statement appears to dismiss the NOL theory, and again unequivocally point the finger toward an explosion forward:
At the time of her sinking, there were 99 crewmen aboard USS Scorpion. The boat contained a treasure-trove of highly sophisticated spy gear and spy manuals, two nuclear-tipped torpedoes, and a nuclear propulsion system. The best available evidence indicates that Scorpion sank in the Atlantic Ocean on May 22, 1968 at approximately 1844Z after an explosion of some type, while in transit across the Atlantic Ocean from Gibraltar to her home port at Norfolk, Virginia.
Several hypotheses about the cause of the loss have been advanced. Some have suggested that hostile action by a Soviet submarine caused Scorpion's loss (see discussion of Offley's "Scorpion Down," below). Shortly after her sinking, the Navy assembled a Court of Inquiry to investigate the incident and to publish a report about the likely causes for the sinking. The court was presided over by VADM Bernard Austin who presided over the inquiry into the loss of the USS Thresher. The panel's conclusions, first printed in 1968, were largely classified. At the time, the Navy quoted frequently from a portion of the 1968 report that said no one is likely ever to "conclusively" determine the cause of the loss. The Clinton Administration declassified most of this report in 1993, and it was then that the public first learned that the panel considered that a possible cause of the malfunction was one of Scorpion's own torpedoes. (The panel qualified its opinion saying the evidence it had available could not lead to a conclusive finding about the cause of her sinking.) However, the Court of Inquiry did not reconvene after the 1969 Phase II investigation, and did not take testimony from a group of submarine designers, engineers and physicists who spent nearly a year evaluating the data.
Today, the wreck of the Scorpion is reported to be resting on a sandy seabed at the bottom of the Atlantic Ocean in approximately 3000 m of water. The site is reported to be approximately 400 miles (740 km) southwest of the Azores Islands, on the eastern edge of the Sargasso Sea. The U.S. Navy has acknowledged that it periodically visits the site to conduct testing for the release of nuclear materials from the nuclear reactor or the two nuclear weapons aboard her, and to determine whether the wreckage has been disturbed. The Navy has not released any information about the status of the wreckage, except for a few photographs taken of the wreckage in 1968, and again in 1985 by deep water submersibles.
The Navy has also released information about the nuclear testing performed in and around the Scorpion site. The Navy reports no significant release of nuclear material from the sub. The 1985 photos were taken by a team of oceanographers working for the Woods Hole Oceanographic Institution in Woods Hole, Massachusetts. The circumstances of the Woods Hole mission show the high level of secrecy the Navy attaches to Scorpion; at the time the photographs were taken, the Navy and Woods Hole both maintained that the Woods Hole team was searching for the wreckage of the noted sunken ocean liner, RMS Titanic. It was only after newspapers learned and reported that the Woods Hole team was also searching for Scorpion that the Navy admitted as much, and released some of the photographs taken during the expedition.
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Another problem with the torpedo theory is that numerous safeguards are in place that would enable the torpedomen to disable the warhead if it were launched and its anti-circular run switch also failed, allowing it to strike its mother ship without detonating, in which case the weapon would thud harmlessly off the hull. Few torpedomen familiar with the Mark 37 have expressed confidence in the self-destruction-by-torpedo theory.
In Silent Steel, Fountain reveals he does not believe Scorpion was sunk by her own torpedo, and during the Court of Inquiry, physicists and engineers who carried out the simulations demanded by Dr. Craven testified that the massively complex simulations, using the crude computing power of the day, were of little value since they were so speculative. This testimony brought a rebuke from the court's members who were sufficiently persuaded by Craven's theories to list them foremost above all others. What has become apparent is that many investigators, even according to a Navy history of the investigation, were upset by Craven's devotion to his hot-running torpedo theory.
Dr. John Craven mentions that he did not work on the Mark 37 torpedo's propulsion system and only became aware of the possibility of a battery explosion twenty years after the loss of the Scorpion. In his book The Silent War, he recounts running a simulation with former Scorpion Executive officer Lt. Cdr. Robert Fountain, Jr. commanding the simulator. Fountain was told he was headed home at 18 knots (33 km/h) at a depth of his choice, then there was an alarm of "hot running torpedo". Fountain responded with "right full rudder", a quick turn that would activate a safety device and keep the torpedo from arming. Then an explosion in the torpedo room was introduced into the simulation. Fountain ordered emergency procedures to surface the boat, stated Dr. Craven, "but instead she continued to plummet, reaching collapse depth and imploding in ninety seconds — one second shy of the acoustic record of the actual event."
Craven, who was the Chief Scientist of the Navy's Special Projects Office, which had management responsibility for the design, development, construction, operational test and evaluation and maintenance of the Polaris Fleet Missile System - at the time of Scorpion's sinking the most technically advanced military system ever deployed - had long believed Scorpion was struck by her own torpedo, but revised his views during the mid-1990s when engineers testing Mark 46 batteries at Keyport, Washington, said the batteries leaked electrolyte and sometimes burned while outside of their casings during lifetime shock, heat and cold testing. Although the battery manufacturer was accused of building bad batteries, it was later able to successfully prove its batteries were no more prone to failure than those made by other manufacturers. In fact, the batteries suspected of being unreliable were manufactured too late to have been installed in Scorpion's torpedoes.
The Navy failed to inform the public that both the U.S. Submarine Force Atlantic and the Commander-in-Chief U.S. Atlantic Fleet opposed Craven's torpedo theory as unfounded and also failed to disclose that a second technical investigation into the loss of Scorpion completed in 1970 actually repudiated claims that a torpedo detonation played a role in the loss of the Scorpion. Despite the second technical investigation, the Navy continues to attach strong credence to Craven's view that an explosion destroyed her, as is evidenced by this excerpt from a May 2003 letter from the Navy's Submarine Warfare Division (N77), specifically written by Admiral P.F. Sullivan on behalf of VADM John J. Grossenbacher (Commander Naval Submarine Forces), the Naval Sea Systems Command, Naval Reactors, and others in the US Navy regarding its view of alternate sinking theories:
Some erroneously claim VADM Grossenbacher's (and Adm. Sullivan's) determination is drawn solely from the inconclusive Findings of Fact, generated by the US Navy's Court of Inquiry into the Scorpion sinking. This is untrue, as their letter (see excerpt below) explicitly mentions their review of a secondary study by the Structural Analysis Group in 1970, and a later report by Dr. Robert Ballard, whose investigative team visited the Scorpion wreck in the 1980s.
Released in 2006, Stephen Johnson’s Silent Steel: The Mysterious Death of the Nuclear Attack Sub USS Scorpion provides a meticulously detailed listing of every mechanical problem on the submarine cited by the Navy or mentioned in crewmen's letters, but ultimately fails to provide any explanation for Scorpion's sinking. Johnson, a critic of Dr. Craven, agrees with Navy scientists who, in 1970, gave their opinion that the sub’s hull was smashed by implosion damage and not a torpedo blast, a finding they support with their interpretation of certain evidence about the condition of the hull and hydroacoustic recordings of the disaster. Silent Steel portrays an overworked submarine denied needed maintenance and manned by a demoralized crew, a depiction contradicted by many former Scorpion enlisted men and officers, and based in part on the testimony of sailors who had applied for transfer from the boat. Johnson also enumerates many of the Navy-wide submarine maintenance issues that denied the Scorpion an overhaul and overdue safety improvements, though the Navy would maintain that virtually all necessary and vital improvements and repairs were made on the submarine before her final deployment. The Submarine Safety Program, initiated following the 1963 loss of the USS Thresher, delayed new submarine construction and sub overhauls by monopolizing skilled workers and critical spare parts. Fearing that a normal overhaul and safety work during 1967 might sideline the Scorpion for three years, it was selected for a brief experimental overhaul, but this was cancelled due to a shortage of workers. The Scorpion sank eight months after leaving Norfolk Naval Shipyard.
In 1999, two New York Times reporters published Blind Man's Bluff, a book providing a rare look into the world of nuclear submarines and espionage during the Cold War. One lengthy chapter deals extensively with Scorpion and her loss. The book reports that concerns about the Mk 37 conventional torpedo carried aboard Scorpion were raised in 1967 and 1968, before Scorpion left Norfolk for her last mission. The concerns focused on the battery that powered the torpedoes. The battery had a thin metal-foil barrier separating two types of volatile chemicals. When mixed slowly and in a controlled fashion, the chemicals generated heat and electricity, powering the motor that pushed the torpedo through the water. But vibrations normally experienced on a nuclear submarine were found to cause the thin foil barrier to break down, allowing the chemicals to interact intensely. This interaction generated excessive heat which, in tests, could readily have caused an inadvertent torpedo explosion. The authors of Blind Man's Bluff were careful to say they could not point to this as the cause of Scorpion’s loss — only that it was a possible cause and that it was consistent with other data indicating an explosion preceded the sinking of Scorpion. Notably, the authors cite examples of hot running torpedo incidents that had occurred on other US submarines prior to the loss of Scorpion. (Although none of those incidents caused the loss of a submarine.)
In 2005, the book Red Star Rogue: The Untold Story of a Soviet Submarine's Nuclear Strike Attempt on the U.S., by former American submariner Kenneth Sewell in collaboration with journalist Clint Richmond, claimed K-129 was sunk 300 miles (560 km) northwest of Oahu on 7 March 1968 while attempting to launch her three ballistic missiles, in a rogue attempt to destroy Pearl Harbor.
In 1995, when Peter Huchthausen began work on a book about the Soviet underwater fleet, he interviewed former Soviet Admiral Victor Dygalo, who stated that the true history of K-129 has not been revealed because of the informal agreement between the two countries' senior naval commands. The purpose of that secrecy, he alleged, is to stop any further research into the losses of either Scorpion or K-129. Huchthausen states that Dygalo told him to "forget about ever resolving these sad issues for the surviving families.
Ed Offley, a reporter on military affairs, has closely followed developments in information concerning the sinking of the Scorpion. His most recent article on the subject is "Buried at Sea" published in the Winter 2008 issue of the Quarterly Journal of Military History. This article summarizes the facts in the case as presented in his 2007 book Scorpion Down: Sunk by the Soviets, Buried by the Pentagon: The Untold Story of the USS Scorpion. In the book Offley, gathering decades of his own research, hypothesizes that the Scorpion was sunk by the Soviets, possibly in retaliation for the loss of the K-129 Golf-II ballistic missile submarine earlier that year. The book paints a picture of increasing Soviet anger at US Navy provocations (specifically close-in monitoring of Soviet naval operations by almost every US nuclear submarine). At approximately the same time, the Soviet intelligence community scored a huge boon in receiving the mechanical cryptologic devices from the USS Pueblo. These machines, combined with daily crypto keys from the John Anthony Walker spy ring, likely allowed the Soviets to monitor in real time U.S. Navy ship dispositions and communications. It is Mr. Offley's contention that the Scorpion was tracked by several Soviet Navy assets from the Mediterranean to its final operational area south of the Azores, where it was then sunk by a Soviet torpedo. Among the oral testimony relied upon by Mr. Offley are recountings of SOSUS recording documenting torpedo sounds, evasion sounds, an explosion, and eventually the sounds of implosions as the Scorpion plunged past crush depth.
This book was written by Kenneth R. Sewell, a nuclear engineer and a U.S. Navy veteran who spent five years aboard the USS Parche (SSN-683), a fast attack submarine. This book attempts to link the sinking of the USS Scorpion with the USS Pueblo Incident, the John Anthony Walker spy ring, and Cold War Soviet aggression, The thesis of this book is that action off the Canary Islands was the direct cause of the sinking. This book purports that this is supported by motives in the Soviet Navy following the sinking of the Soviet submarine K-129 (Golf II), which caused the Russian Navy to trap a US submarine. The bait for this trap would be strange military operations and furtive naval maneuvers in the Atlantic, accompanied by countermeasures that would only seemingly be defeated by the deployment of a nuclear submarine. With information from spying by Walker, the position and arrival time of the Scorpion was known by the Russians, and its sinking followed the springing of the trap. The book then purports a cover-up by American and Soviet officials, to avoid public outrage and an increase in Cold War tension.