Following action at Saipan, Stump retained commanded Carrier Division 24 but was now assigned to Task Unit 77.4.2 ("Taffy II"). At the battles of Leyte Gulf and Samar he embarked aboard the in October 1944. For his role in these battles he was awarded the Navy Cross. His flag remained on "Natoma Bay" through early 1945 while his sailors continued operations in the Philippines.