Following the Gold Crew's successful Polaris missile launch on 16 December 1964, Stonewall Jackson returned to the Pacific Ocean to complete shakedown operations.

She began post-shakedown alterations and repairs on 13 February 1965, then made final preparations at Bangor, Washington for an overseas deployment.

On 23 April 1970, she got underway from Pearl Harbor, Hawaii, to conduct a special operation, before continuing on to the Panama Canal.

On 15 July she entered the shipyard of the Electric Boat Division of General Dynamics at Groton, Connecticut, for conversion to carry the Poseidon C-3 ballistic missile system.

On 7 April 1971, Stonewall Jackson got underway for Charleston for ballistic missile loading in preparation for her first post-conversion and first Atlantic deterrent patrol.

She returned to the United States for an extensive overhaul at Portsmouth, New Hampshire Shipyard and was fitted with the Trident C-4 missile system at Pier side Port Canaveral, Florida in late 1988.