Upon finishing her repairs, "Fanshaw Bay" continued acting as the flagship of Carrier Division 25, now under the command of Rear Admiral Clifton A. F. Sprague. After departing from Pearl Harbor, she arrived at Manus Island, of the Admiralty Islands. "Fanshaw Bay", along with five other escort carriers and a screen of eight destroyer escorts, was assigned to Task Group 77.1, which would support the landings on Morotai. Notably, her aircraft contingent had been swapped, and she now hosted Composite Squadron 66 (VC-66). She departed Manus on 10 September, and she began air support operations on 15 September. On 17 September, two Avengers, one from "Fanshaw Bay", collided while moving into formation on an antisubmarine patrol. Of the six men involved, only a single survivor was recovered by the submarine chaser . On 19 September, "Fanshaw Bay" lost another aircraft, with one of her Wildcats, diving on a Zero, missing and exploding on contact with the water. The carrier continued to hemorrhage aircraft, with an additional two fighters and a torpedo bomber crashing by 27 September.