Proteus was damaged in collision with an Admiralty tug at Malta; local repairs allowed her to complete patrols in the Straights of Messina and the coasts of Calabria and Libya, but in November she was ordered back to Britain for a refit at Portsmouth Naval Base which lasted until July 1941.

Returning to active patrols in late October, her sinking of the troop transport ship Ithaka on 10 November[2] is thought to be the first radar guided submarine attack.

[3] In the early hours of 8 February 1942 off the Greek island of Lefkada, Proteus sighted a dark shape astern, thought initially to be an enemy submarine.

[2] After a total of fourteen war patrols in the Mediterranean, the last cut short by engine problems, Proteus was ordered to return to Britain in September 1942.

After a lengthy refit at Devonport Naval Base which completed in May 1943, she was assigned to training duties, mainly in the River Clyde area, which continued until she was decommissioned on 30 June 1944.