[45] He then led three Huckins PT boats—PT-98, PT-99, and PT-101, which were being relocated from MTBRON 4 in Melville, Rhode Island, back to Jacksonville, Florida, and the new MTBRON 14 (formed February 17, 1943). During the trip south, he was hospitalized briefly in Jacksonville after diving into the cold water to unfoul a propeller. Thereafter, Kennedy was assigned duty in Panama and later in the Pacific theater, where he eventually commanded two more PT boats.[46]

Commanding PT-109
Kennedy on his navy patrol boat, the PT-109, 1943
In April 1943, Kennedy was assigned to Motor Torpedo Squadron TWO,[39] and on April 24 he took command of PT-109,[47] which was based at the time on Tulagi Island in the Solomons.[40] On the night of August 1–2, in support of the New Georgia campaign, PT-109 was on its 31st mission with fourteen other PTs ordered to block or repel four Japanese destroyers and floatplanes carrying food, supplies, and 900 Japanese soldiers to the Vila Plantation garrison on the southern tip of the Solomon's Kolombangara Island. 