In December 1958, he assumed command of Carrier Division Four, and a year later, on January 25, 1960, he was named Assistant Chief of Naval Operations for Plans and Policy. On December 15, 1961, he was promoted to vice admiral and a month later became Deputy Director of Joint Strategic Target Planning, headquartered at Offutt Air Force Base, Omaha, Nebraska. While in this capacity, Johnson was the Navy's senior representative in determining U.S. air strike priorities during the 1962 Cuban Missile Crisis.