For her last voyage, the SS Thistlegorm set sail from Glasgow on 2 June 1941. She was destined for Alexandria carrying supplies to relieve the 8th Army in preparation for Operation Crusader. Germany was controlling the Mediterranean Sea during this period, a convoy of ships sailed around the Cape to the Red Sea.
The Suez Canal at that time was closed as a result of a ship collision and Captain Ellis anchored the Thistlegorm near Shag Rock. She held the position for over two weeks, moored at this supposedly safe position. She like many others were awaiting instructions to proceed through the canal. The bombers were returning from a sortie looking for a large troop carrier, which they didn't find. As they were running low on fuel, they turned around and stumbled upon the Thistlegorm. She was a sitting duck for two German bombers returning to Crete. They dropped two 1,000 lb (450 kg) bombs directly onto the ship penetrating No. 4 Hold, which was holding the ammunition.
The resulting explosion killed nine crew members and was so forceful that it launched two railway locomotives stacked on deck into the air. They currently stand upright alongside the wreck at a depth of 33m. Thistlegorm sank immediately, leaving no time for the crew to operate the lifeboats. Instead, they jumped into the water and were later rescued by the HMS Carlisle, another British ship moored nearby.
In the early fifties Jacques-Yves Cousteau "discovered" her by using information from local fishermen. Contrary to popular belief, he was actually asked to assess the wreck as she was considered a potential hazard to shipping.
He raised several items from the wreck, including a motorcycle, the Captain’s safe, and the ship’s bell. The February 1956 edition of "National Geographic" clearly shows the ship’s bell in place and Cousteau's divers in the ship’s "Lantern Room".