Grey Havoc

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HMS Alliance was modified for SIGINT/ELINT work during a yard period in the late 1950s (1958-1960), in particular for monitoring the Soviet Northern Fleet, at least according to the Daily Telegraph obituary of Rear Admiral Martin Wemyss linked below:
Wemyss’s next appointment was at the submarine desk in Naval Intelligence (1958-60), ideal preparation for his command of Alliance, a submarine specially fitted for covert surveillance of the Soviet navy on exercise in the Arctic.

The Wikipedia entry on Alliance makes mention of the overhaul and some of its details but not its purpose, though it does mention in passing an interesting temporary assignment later on during the early 1960s:
Between 1958 and 1960 Alliance was extensively modernised by having the deck gun and external torpedo tubes removed, the hull streamlined and the fin replaced with a larger (26 feet 6 inch high), more streamlined one constructed of aluminium. The purpose of these modifications was to make the submarine quieter and faster underwater. Following the modifications, the wireless transmitting aerial was supported on a frame behind the fin but was later replaced with a whip aerial on the starboard side of the fin which could be rotated hydraulically to a horizontal position.

The original gun access hatch was retained, however, allowing Alliance to be equipped with a small calibre deck gun again when serving in the Far East during the Indonesian Confrontation of the earlier 1960s.[2]

In May 1961 the pennant numbers of British submarines were changed so that all surviving submarines completed after the Second World War were now numbered from S01 upwards, and Alliance was given the number S67.
 
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