It was her own demise that made her most famous. At about 05:00 on 30 October 1942, U-559 was spotted by a Royal Air Force Sunderland, W from 201 Squadron in position 31°47′N 33°24′E, 70 miles north of the Nile Delta. The destroyer HMS Hero was alerted by radio and steamed to intercept her, while the destroyers HMS Petard, Pakenham, Dulverton and Hurworth sailed from Port Said, Egypt. At about 12:34 a Wellesley patrol aircraft, F from 47 Squadron, spotted the periscope of the submerged U-559 and attacked with depth charges.
The destroyer group hunted for the U-boat for 16 hours, constantly depth charging. After dark, U-559, with a cracked pressure hull, unable to maintain level trim and four of her crew dead from explosions and flooding, was forced to the surface. She was close to Petard, which immediately opened fire with her Oerlikon 20 mm cannon.
The German crew hurriedly scrambled overboard without destroying their codebooks or Enigma machine and, crucially, having failed to open sea-water vents to properly scuttle the U-boat. Three Royal Navy sailors, Lieutenant Anthony Fasson, Able Seaman Colin Grazier and NAAFI canteen assistant Tommy Brown, then boarded the abandoned submarine. There are differing reports as to how the three British men boarded the U-boat. Some accounts say that they “swam naked” (such as that of Kahn), to U-559 but Sebag-Montefiore states that they either leapt from Petard or, in Brown’s case, from a whaler, which was sinking, but slowly. They retrieved the U-boat’s Enigma key setting sheets with all current settings for the U-boat Enigma network. Two German crew members, rescued from the sea, watched this material being loaded into Petard’s whaler but were dissuaded from interfering by an armed guard. Grazier and Fasson were inside the boat, attempting to get out, when the U-boat foundered; both drowned.