Implosion not Explosion
USS Thresher lost propulsion as a result of a reactor scram. The weld on one of the cooling pipes is believed to failed causing a lose of cooling pressure which shut down the reactor.
With a loss of propulsion the crew would have tried to clear ballast to float back to the surface, but ice is believed to have formed in the pipes preventing the ballast from being cleared.
So the ship sank past its crush depth and imploded.
It had imploded. When the hull finally gives way, the the implosion is so fast that air/oxygen within the vessel spontaneously ignites from the heat of the compression.
The shock of such rapidly collapsing water is so severe that it resembles an explosion on hydrophones (underwater microphones).
If there were a secondary explosion, it would have been from an explosive onboard misfiring (scuttling charges or a torpedo). But that’s not necessary to jet parts of the imploded submarine outward – the momentum of incoming water will continue tearing through what hadn’t ruptured already.
From https://web.archive.org/web/20131031061419/http://www.navsource.org/archives/08/08593b.htm :
> Measurements made during the lowering and recovery of an instrumented diesel submarine to collapse depth are consistent with the conclusion that the water-ram produced by the initial breaching of the Thresher pressure hull at 2400 feet traversed the diameter of the pressure hull in about 0.005 seconds (five milliseconds), a velocity of about 4000 mph. That force would have torn the pressure hull longitudinally and vertically as verified by imagery of the Thresher wreckage. Even allowing for differences in pressure hull design, the extent of the damage to Thresher, compared to the Scorpion, which collapsed at 1530 feet, indicates Thresher collapsed at significantly greater depth.
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