Following completion of the US Army Command and General Staff Course and promotion to lieutenant colonel, Wilson was assigned in June 1959 as Director of Instruction of the US Army Special Warfare School, Fort Bragg, NC. Over the next two years, he gained considerable notoriety for his foundational work on doctrine for small wars, insurgency and counter-insurgency. In June 1961, he was appointed Deputy Assistant to the Secretary of Defense for Special Operations, serving in that capacity for the next two years and playing a key staff support role at such critical moments as the Cuban Missile Crisis of October 1962.