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From Holy Loch, "Alexander Hamilton" conducted her 39th and 40th deterrent patrols. She departed Holy Loch in May 1978 for her 41st deterrent patrol and concluded it at Charleston in July 1978. She remained there until August 1978 when she got underway for New London. She arrived at New London early in September 1978 and, after exchanging crews, embarked upon her 42nd deterrent patrol later that month. She ended that patrol at Holy Loch in October 1978. Over the next year, she made four patrols from Holy Loch. On 31 October 1979, she departed Holy Loch on her 46th deterrent patrol, ending it at Charleston on 7 December 1979. Early in January 1980, she departed Charleston on her 47th deterrent patrol. She concluded that patrol at Holy Loch on 17 March 1980 and operated from that base for the remainder of 1980.