VF-84 last deployment with the Crusader ended on March 4 1964. During that cruise VF-41, the all-weather fighter squadron of CVG-7, was already flying the F-4B Phantom II. VF-84 missed the next cruise of the USS Independence, while transitioning to a new aircraft, new weapons system and new mission. The squadron started its long association with the McDonnell F-4 Phantom II in June 1964.

The Bones made a spectacular return to naval aircraft at that time, with the first F-4Bs of VF-84 displaying a waving Jolly Rogers over their tail surfaces. Flamboyant color schemes were not lacking on the US Navy at the time, but this one made a lasting impression.