[60] On October 8, 1943, Kennedy was promoted to full lieutenant.[61] On November 2, Kennedy's PT-59 took part with two other PTs in the successful rescue of 40–50 marines. The 59 acted as a shield from shore fire and protected them as they escaped on two rescue landing craft at the base of the Warrior River at Choiseul Island, taking ten marines aboard and delivering them to safety.[62][63] Under doctor's orders, Kennedy was relieved of his command of PT-59 on November 18, and sent to the hospital on Tulagi.[64] From there he returned to the United States in early January 1944. After receiving treatment for his back injury, he was released from active duty in late 1944.[65]
Kennedy was hospitalized at the Chelsea Naval Hospital in Chelsea, Massachusetts from May to December 1944.[39] On June 12, he was presented the Navy and Marine Corps Medal for his heroic actions on August 1–2, 1943, and the Purple Heart Medal for his back injury while on PT-109.[66] Beginning in January 1945, Kennedy spent three more months recovering from his back injury at Castle Hot Springs, a resort and temporary military hospital in Arizona.