He was assigned to Torpedo Squadron (VT-51) as the photographic officer in September 1943. The following year, his squadron was based on the USS San Jacinto as a member of Air Group 51, where his lanky physique earned him the nickname 'Skin'. During this time, the task force was victorious in one of the largest air battles of World War II: the Battle of the Philippine Sea.
After Bush's promotion to Lieutenant Junior Grade on August 1, the San Jacinto commenced operations against the Japanese in the Bonin Islands. Bush piloted one of four Grumman TBM Avenger aircraft from VT-51 that attacked the Japanese installations on Chichijima. His crew for the mission, which occurred on September 2, 1944, included Radioman Second Class John Delaney and Lieutenant Junior Grade William White. During their attack, the Avengers encountered intense anti-aircraft fire; Bush's aircraft was hit by flak and his engine caught on fire. Despite his plane being on fire, Bush completed his attack and released bombs over his target, scoring several damaging hits. With his engine afire, Bush flew several miles from the island, where he and one other crew member on the TBM Avenger bailed out of the aircraft; the other man's parachute did not open. It has not been determined which man bailed out with Bush as both Delaney and White were killed as a result of the battle. Bush waited for four hours in an inflated raft, while several fighters circled protectively overhead until he was rescued by the lifeguard submarine USS Finback. For the next month he remained on the Finback, and participated in the rescue of other pilots.
Ensign Bush was assigned to the torpedo squadron VT-51, based in the Pacific. The first casualty in their unit was the crew aboard a plane flown by Jim Wykes, Bush's close friend and roommate aboard the aircraft carrier. There was no distress signal. The plane simply disappeared from radar. Bush recalls curling up on his cot and crying when it became clear the crew would not return. On September 2, 1944, Bush's plane was shot down in a bombing run over the island of Chichi Jima, a key location for Japanese operations in the Pacific. Bush and one of his crewmen bailed out, but the other man's parachute never opened. The third crewman went down with the plane. Alone in the ocean off the coast of Chichi Jima, Bush was eventually rescued by an American submarine on patrol for downed pilots. More than fifty years later, Bush said the deaths of his two crewmen "still weigh heavy on my mind."
He served in the Navy during World War II from 1942 until September 1945. When he became a pilot in July 1943, he was the youngest pilot in the Navy. He flew torpedo bombers in the Pacific theater and went on fifty-eight combat missions during the war. On September 2, 1944, while flying a mission to bomb an enemy radio site, his plane was shot down by Japanese fire; Bush bailed out over the ocean. He was rescued by a submarine a short time later and was awarded the Distinguished Flying Cross for heroism under fire.