On one of her North Sea patrols on 4th December 1939, HMS Nelson entered Loch Ewe at 13 knots, passing over a magnetic mine and activating it. She was lifted and shaken by the tremendous explosion. No one was killed, but there were 73 casualties. In the heads forward, many toilets shattered and the occupant suffered severe lacerations. The ship’s bottom was torn in several places, mainly to the starboard outer plating for a distance of 70 feet which was forced inward by about 4 feet. Flooding extended over a distance of 140 feet. There was also shock damage to the ammunition supply machinery.

A young Lieutenant aboard was sent to Pool House to report the incident. Later he would be promoted to Lt. Commander Stevenson and put in charge of the Loch Ewe Boom Defense. Winston Churchill referred to Nelson as “our interesting invalid”. She managed to return to harbour under the utmost secrecy to HM Dockyard Portsmouth to spend the next eight months in dock being repaired and refitted.

Lieutenant Johannes Hakebost of U-31 left Willshaven on the 9th of September 1939 to start his campaign in the Battle of the Atlantic. Just eight days after the start of the war U-31 became the first submarine to sink a merchant ship in WW2. It was on her third patrol, on 27th October, that she laid the minefield in Loch Ewe that caught the Nelson.
In December 1939 U-31 had more success, sinking six ships in six days. After this patrol she returned to Loch Ewe to lay more mines but to no avail. On 28th January 1940, her crew realised the drinking water on board was contaminated and returned to home port. She spent a month there undertaking repairs.

On 11th March 1940 her captain took her out for sea trials. At around noon a Bristol Blenheim bomber from No. 82 Squadron, dropped two direct bombs causing her sinking. She was the first German U-boat to be sunk in WW2 by an overhead aircraft attack. In addition to the captain and crew, 13 shipyard workers who had been invited to participate in the sea trials were also lost. A total of 58 men died that day. Hakebost was aged 33.
Unfortunately for U-31, she would have the curious distinction of being sunk twice in WW2. Four months after the first sinking, she was raised and refurbished and in October 1940 went out on patrol with a new commander, Wilfried Prellberg. The patrol would only last 15 days, however, as on 2nd November U-31 was sunk off Ireland by HMS Antelope and Achates, whose depth charges forced her to the surface. Antelope rescued 44 of her crew (from a total of 46), of which one died the following day.
In her seven patrols U-31 sank 11 Merchant ships totalling just under 28,000 gross tons as well as two auxiliary warships, HMT Glen Albyn and HMT Promotive, both requisitioned trawlers based in Loch Ewe. It was responsible for the mining of HMS Nelson, and also the damage to HMS Antelope, which collided with the U-boat whilst trying to board the unmanned submarine the day after she picked up the crew. It was this collision that caused the second sinking of U-31. The submarine was lost, and Antelope limped home to the Clyde to be repaired.