Please find my answer to this question originally asked and answered on Quora below:

USS Scorpion is one of two nuclear submarines the U.S. Navy has lost, the other being USS Thresher. It was one of four mysterious submarine disappearances in 1968, the others being the Israeli submarine INS Dakar, the French submarine Minerveand the Soviet submarine K-129.

From USS Scorpion (SSN-589)

French submarine Minerve (S647) — Wikipedia Seems likely a combination of snorkel and bad weather.

Flore, sister ship of Minerve

On January 27, 1968, at 07:55 hrs, Minerve was travelling just beneath the surface of the Gulf of Lion using her snorkel, roughly 25 nautical miles (46 km) from her base in Toulon, when she advised an accompanying Breguet Atlantic aircraft that she would be at her berth in about an hour. However, this was the last time the boat and her crew of six officers and 46 sailors were seen. She disappeared in waters between 1,000 metres (3,300 ft) and 2,000 metres (6,600 ft) deep.

Commander Philipe Bouillot later said that Minerve’s new captain Lieutenant André Fauve had spent 7,000 hours submerged over four years on submarines of the same class and never had a problem. The only factor known that could have caused her to sink was the weather, which was extremely bad at the time of her loss.

The French Navy promptly launched a search for the missing submarine mobilizing numerous ships, including the aircraft carrier Clemenceau and the submersible SP-350 Denise under the supervision of Jacques Cousteau, but found nothing and the operation was called off on 2 February. However, the search for Minerve, under the name Operation Reminercontinued into 1969 and utilized the submersible Archimède with the U.S. survey ship USNS Mizar. To this day no trace of the vessel has been found.

INS Dakar — Wikipedia — Appears may have been a case of diving in area shallower than minimum required/recommended depth.

General Azab mentioned that the submarine may have crashed into the seabed due to the shallow depth of water in that region, about 36 meters, while it needed at least 40 meters to dive. It appears that the submarine commander took the risk.

At 06:10 on 24 January 1968 Dakar transmitted her position, 34.16°N 26.26°E, just east of Crete. Over the next 18 hours she sent three control transmissions which did not include her position. Her final broadcast was at 00:02 25 January, after which no further transmissions were received.

On 26 January the British Admiralty reported the submarine was missing and gave the last known position as 100 miles (160 km) west of Cyprus. An international search and rescue operation began, including units from Israel, the United States, Greece, Turkey, Britain and Lebanon. Although the Israeli Navy in Haifa began broadcasting calls to commercial vessels to be on the look out for Dakar, Israeli officials would not admit the submarine was missing. On 27 January, a radio station in Nicosia, Cyprus, received a distress call on the frequency of Dakar’s emergency buoy, apparently from south-east of Cyprus, but no further traces of the submarine were found. On 31 January, all non-Israeli forces abandoned their search at sunset. Israeli forces continued the search for another four days, ceasing at sundown on 4 February 1968.

Israel denied that Dakar sank as the result of hostile action and stated that Dakar was involved in crash diving exercises on its return voyage and was lost probably as a result of a mechanical failure. On 25 April 1968, Vice Admiral Abraham Botzer, commander of the Israeli Navy, stated that Dakar sank on 24 January 1968, two days before being reported missing due to “technical or human malfunctioning” and not “foul play”.

Soviet submarine K-129 (1960) — Wikipedia

Several theories

The official Soviet Navy hypothesis is that K-129, while operating in snorkel mode, slipped below its operating depth. Such an event, combined with a mechanical failure or improper crew reaction, can cause flooding sufficient to sink the boat.

This account, however, has not been accepted by many, and four alternative theories have been advanced to explain the loss of K-129:

  1. A hydrogen explosion in the batteries while charging;
  2. A collision with USS Swordfish;
  3. A missile explosion caused by a leaking missile door seal;
  4. Intentional or unintentional scuttle by crew due to K-129 violating normal operating procedures and/or departing from authorised operating areas.

Reportedly, as many as 40 of the complement of 98 were new to the submarine for this deployment.

K-129 was approximately midway through standard shore leave/replenishment and repair when a new mission was tasked.

Note an additional explanation was provided in the comments that I thought was worth adding to the body of the answer.

Regarding K-129 there has been more information declassifide as of late that suggest the loss was do to a missle warhead’s non-nuclear high explosive lense detonated causing a rupture of the pressure hull just aft of the con. The reason for the detonation is presently hotly contested. One theory is agents of the KGB took control of the sub and attempted a non-sanctioned attack on Hawaii. As the wreck was found over a thousand miles south of it’s normal operating box this theory has gained quite a bit of legs. Unless Putin declassifies the KGB and old Soviet naval records we nay never know the true fate of K-129.

USS Scorpion (SSN-589) — Wikipedia Several theories but likely to be a torpedo explosion.

A later theory was that a torpedo may have exploded in the tube, caused by an uncontrollable fire in the torpedo room. The book Blind Man’s Bluff documents findings and investigation by Dr. John Craven, who surmised that a likely cause could have been the overheating of a faulty battery.

The Mark 46 silver–zinc battery used in the Mark 37 torpedo had a tendency to overheat, and in extreme cases could cause a fire that was strong enough to cause a low-order detonation of the warhead. If such a detonation had occurred, it might have opened the boat’s large torpedo-loading hatch and caused Scorpion to flood and sink. However, while Mark 46 batteries have been known to generate so much heat that the torpedo casings blistered, none is known to have damaged a boat or caused an explosion.

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 Scorpion. In his book The Silent War, he recounts running a simulation with former Scorpion executive officer Lieutenant Commander 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 UGM-27 Polaris Fleet Missile System had long believed Scorpion was struck by her own torpedo, but revised his views during the mid-1990s when he learned that engineers testing Mark 46 batteries at Keyport, Washington just before the Scorpion’s loss, said the batteries leaked electrolyte and sometimes burned while outside 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.

The results of the U.S. Navy’s various investigations into the loss of Scorpion are inconclusive. While the court of inquiry never endorsed Dr. Craven’s torpedo theory regarding the loss of Scorpion, its “findings of facts” released in 1993 carried Craven’s torpedo theory at the head of a list of possible causes of Scorpion’s loss.

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