On 9 February 1959, "Grayback" departed Mare Island to make Pearl Harbor her permanent home base, reaching Hawaii on 7 March via Port Hueneme, California, Long Beach, California, and Mazatlan, Mexico. After a series of exercises there, she cruised to Dutch Harbor, Umak Island, Sequam Island, and Kodiak, Alaska, for further missile exercises from 3–31 July. This was followed by the first of her nine deterrent missile strike missions, from 21 September to 12 November. "Grayback"s first patrol terminated at Yokosuka, Japan, as did two others. She returned to Pearl Harbor 8 December.