Joe Kennedy was totally involved with JFK's naval career from the beginning:
JFK applied for a commission after Pearl Harbor--college grads routinely got quickie commissions in those days. He was rejected for poor health (a lot worse than he ever let on in his lifetime), but the old man pulled strings and got him his commission, as well as a plum intelligence assigment in Washington DC. But JFK was cavorting with Inga Arvad, a Scandinavian journalist who was being watched by the FBI as a possible Nazi spy. They reported JFK's liaisons to Naval Intelligence. A mere mortal would have been court-martialed, but JFK was banished to an obscure post in South Carolina.

Then fate intervened. The Navy decided to deploy PT boats in the Pacific. They were like medium-sized yachts--fast, maneuverable, and capable of getting close to Japanese warships, launching torpedoes, and getting away quickly. The Navy needed PT captains who had yachting experience, and they weren't too concerned about the captains' health since their anticipated life expectancy in that dangerous assignment wasn't very long. JFK qualified on both counts. PT-109 was rammed by a Japanese destroyer. According to some of his biographers, the ramming was caused by JFK's negligence. There is no doubt that he behaved heroically in swimming several of his injured crewmen to a desert island, where they were rescued by US forces. But there is doubt that his back injury was was solely caused by that incident--some believe that the ramming aggravated a childhood back injury and may have been aggravated his lifelong problem with adrenal insufficiency. And, his discharge from the Navy wasn't a slam-dunk because of his "injury"--Old Man Kennedy arranged for him to be promoted, assigned as a PT instructor in Florida, then discharged before the war's end. He also arranged all the publicity that made JFK a war hero.