In 1967, she received emergency repairs at Norfolk Naval Shipyard and sent back to sea rather than receiving the scheduled extensive overhaul she was due. Later that year, Commander Francis Slattery took command of Scorpion. In February 1968, boat and crew departed for a tour of duty in the Mediterranean. During the assignment, which lasted until May of that year, Scorpion had several mechanical problems.
After a short assignment observing Soviet naval activity near the Azores. While travelling back to the United States after completing her surveillance mission she ran into difficulties. On the night of 20th/21st May her crew repeatedly attempted to contact US Naval Station Rota, Spain but only managed to contact a communications station near Greece. Six days later she had still not arrived at her home-base at Norfolk, Virginia, so naval personnel reported her overdue and began a search.
On 5th June 1968, the US Navy declared Scorpion and her crew of 99 hands “presumed lost.” Later that year, the crew of the Navy’s oceanic research ship Mizar discovered parts of the submarine’s hull 740km south-west of the Azores. To date the US Navy has not confirmed a precise cause of the sinking of USS Scorpion.