After a month at San Pedro Navy Yard for repairs, the overhaul of the BRAINE was complete. In August she departed for Puget Sound to escort the USS SOUTH DAKOTA to Pearl Harbor. In mid-September the BRAINE was part of TG 33.3 and departed Pearl Harbor via Eniwetok to the Admiralty Islands in preparation for the invasion of the Philippine Islands. As the BRAINE crossed the Equator for the second time Neptunus Rex once again visited the ship with great fanfare for the initiation of the Pollywogs, including the Captain, into his underwater domain.
Upon arrival at Manus Island in the Admiralty Islands, the BRAINE loaded with stores and ammunition in preparation for the largest invasion to date - the return of General MacArthur to Philippines - the invasion of Leyte Island. On 20 - 21 October 1944, the BRAINE provided intensive fire support for the ground troops as they landed and repelled several air attacks. The BRAINE was close by as General MacArthur waded ashore and delivered his famous, “I Have Returned” speech.
For the next month the ship provided escort for the re-supply echelons from Admiralty and New Guinea. During one trip a submarine contact was detected and several depth charges were dropped with the results unknown.
On 1 December 1944, the USS BRAINE was detached from DesRon 45 and ordered to join DesRon 23, the famed “Little Beavers” with which she served until the end of the War. On 15 December 1944, the BRAINE was part of the screen and bombardment group for the invasion of Mindoro and had her first experience with kamikaze planes. She was attacked by four planes. The first plane dropped a bomb that landed 100 feet off the starboard quarter. The plane was shot down and three other aerial attackers were driven off.
As the Pacific War progressed the convoys became larger. In early January the BRAINE was ordered to be part of the large convoy enroute to the invasion of Luzon at Lingayen Gulf. On the moonless night of 7 January 1945, off the entrance to Manila Bay, the radar detected a probing by a Japanese destroyer. The protecting escort fired starshells to illuminate the enemy and sank it with devastating fire. The Japanese ship was one of the destroyers of the Hatsuharu class. This was the last engagement between surface ships of World War II. In support of the invasion the BRAINE drove off several air attacks. The ship was grounded on an uncharted shoal and returned to Leyte for repairs in a floating dry-dock, then continued to act as escort for the re-supply echelons.
In mid-February the BRAINE again escorted troop ships and provided close-in fire support for the paratrooper landings on the island of Corregidor. The ship encountered an enemy minefield and destroyed several mines by gunfire. In mid-March the BRAINE escorted troop carriers and provided fire support for the landings at Zambiango on the island of Mindanoa in the southern Philippines.
Meanwhile the invasion at Okinawa was in progress. Destroyers were assigned to picket duty abut forty miles out to act as an early warning radar system. The picket ships were under constant kamikaze attack. As messages were decoded about the action, the names of familiar sister destroyers were listed as casualties. They were either sunk or damaged. In April, fifteen new crew members reported on board the BRAINE. On 13 May LT. Jack B. Lahrmer, USNR reported on board as Executive Officer.
Two days later, the BRAINE with DesRon 23 was ordered to Okinawa.