Following the attack on Pearl Harbor, the Japanese began attacking the Philippine Islands.  In May of 1942, the remaining American and Filipino forces in the area were forced to surrender.  However, the United States began to put a major emphasis on retaking the islands.  Four major battles in the next two and a half years allowed the United States to move into a position to take back the Philippine Islands:  Midway, Coral Sea, Eastern Solomons, and Santa Cruz.  During these battles the Japanese navy lost a great deal of their trained personnel, including most of their carrier aircrew.  The Japanese would never recover from this.  In June of 1944, the battle of the Philippine Sea was fought.  The Japanese sent into battle nine carriers with 473 aircraft aboard.  However, due to the lack of experienced crews, the Japanese forces were massacred.  In the two days of battle, over 400 aircraft and 3 carriers of the IJN,  were lost. This brutal defeat dismantled the ability of the carriers in the IJN.  Further navy battles would be fought mainly with their destroyers, which were still quiet capable. 

Sources:            http://www.odyssey.dircon.co.uk/LEYTE_GULF_Summary_of_the_Battle_.htm