As part of a deception operation when Operation Halberd, another mission to convey troops and supplies to Malta, began on 24 September, Somerville's flag was transferred to "Rodney" while "Nelson" and some escorting destroyers departed Gibraltar heading westwards as if the former ship had relieved the latter. "Rodney" and the rest of Force H headed eastwards with "Nelson" and her escorts joining the main body during the night. The British were spotted the following morning and attacked by (Royal Italian Air Force) aircraft the next day. A Savoia-Marchetti SM.84 torpedo bomber penetrated the screen and dropped a torpedo at a range of . It blew a hole in the bow, wrecked the torpedo compartment and caused extensive flooding; there were no casualties amongst the crew. Although she was down at the bow by and ultimately limited to a speed of to reduce the pressure on her bulkheads, "Nelson" remained with the fleet to so that the Italians would not know that she had been damaged. After emergency repairs were made in Gibraltar, the ship proceeded to Rosyth where she was under repair until May 1942.