It only took Kennedy a month to recover and return to duty, commanding the "PT-59". He and his crew removed the original torpedo tubes and depth charges and refitted the vessel into a heavily armed gunboat, mounting two automatic 40mm guns and ten .50 caliber Browning machine guns. The new plan involved attaching a gunboat to each PT boat section adding gun range and defensive power against barges and shore batteries which the "59" went on to encounter on several occasions from mid-October to mid-November. On October 8, 1943, Kennedy was promoted to full lieutenant. 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. Under doctor's orders, Kennedy was relieved of his command of "PT-59" on November 18, and sent to the hospital on Tulagi. 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.