The US Navy has been rather close-mouthed about it all these years, and now is unwilling to allow robotic submersibles to explore the wreck.
When I was in Cryptologic Technician "A" school in Pensacola, Florida, back in 1981, we had an instructor (can't recall his name now) who had served in submarines and who, one evening while we were all swapping yarns, promised to tell us the "true" story of the USS Scorpion, but only after our security clearances had come through. We never followed up on the story, as I recall, nor did I ever again inquire about it. Always regretted not doing so.
I've always had a sneaking suspicion that RADM. Daniel Gallery, the war hero/novelist, had inside information about the sinking of the Scorpion, and wrote his novel The Brink about a very similar scenario. Just my opinion.