The British campaign against Axis shipping in the fall of 1941 was being prosecuted by both submarines and aircraft. The submarines operated from Gibraltar, Malta, and Alexandria. They were primarily the small U Class boats at this stage. Aerial reconnaissance was photographing ships engaged in the North Africa supply effort to aid analysis.
The Italians ran convoys down through the Straits of Messina to Tripoli and Benghazi. Evasive routing was also employed, so that some ran to the east before they ran back to the Libyan ports. The convoys stayed well away from Malta.
Three British submarine flotillas were involved. They were the 8th Flotilla from Gibraltar, the 10th Flotilla from Malta, and the 1st Flotilla from Alexandria. The 8th flotilla included some Dutch submarines. On 18 September 1941, Upholder sank two Italian liners, the Neptunia and Oceania. Operations occurred with the expected losses: Union was sunk in July, and P32 and P33 were mined off Tripoli in August.
This is based on the account in Vol.II of the Official History.