Douglas MacArthur
Luzon

MacArthur's next move was the invasion of Mindoro, where there were good potential airfield sites. Willoughby estimated, correctly as it turned out, that the island had only about 1,000 Japanese defenders. The problem this time was getting there. Kinkaid balked at sending escort carriers into the restricted waters of the Sulu Sea, and Kenney could not guarantee land based air cover. The operation was clearly hazardous, and MacArthur's staff talked him out of accompanying the invasion on Nashville. As the invasion force entered the Sulu Sea, a kamikaze struck Nashville, killing 133 people and wounding 190 more. Australian and American engineers had three airstrips in operation within two weeks, but the resupply convoys were repeatedly attacked by kamikazes. During this time, MacArthur quarreled with Sutherland, notorious for his abrasiveness, over the latter's mistress, Captain Elaine Clark. MacArthur had instructed Sutherland not to bring Clark to Leyte, due to a personal undertaking to Curtin that Australian women on the GHQ staff would not be taken to the Philippines, but Sutherland had brought her along anyway.

The way was now clear for the invasion of Luzon. This time, based on different interpretations of the same intelligence data, Willoughby estimated the strength of General Tomoyuki Yamashita 's forces on Luzon at 137,000, while Sixth Army estimated it at 234,000. MacArthur's response was "Bunk!". He felt that even Willoughby's estimate was too high. "Audacity, calculated risk, and a clear strategic aim were MacArthur's attributes", and he disregarded the estimates. In fact, they were too low; Yamashita had more than 287,000 troops on Luzon. This time, MacArthur traveled aboard the light cruiser USS Boise, watching as the ship was nearly hit by a bomb and torpedoes fired by midget submarines. His communiqué read: "The decisive battle for the liberation of the Philippines and the control of the Southwest Pacific is at hand. General MacArthur is in personal command at the front and landed with his assault troops."

MacArthur's primary concern was the capture of the port of Manila and the airbase at Clark Field, which were required to support future operations. He urged his commanders on. On 25 January 1945, he moved his advanced headquarters forward to Hacienda Luisita, closer to the front than Krueger's. He ordered the 1st Cavalry Division to conduct a rapid advance on Manila. It reached the northern outskirts of Manila on 3 February, but, unknown to the Americans, Rear Admiral Sanji Iwabuchi had decided to defend Manila to the death. The Battle of Manila raged for the next three weeks. To spare the civilian population, MacArthur prohibited the use of air strikes, but thousands of civilians died in the crossfire or Japanese massacres. He also refused to restrict the traffic of civilians who clogged the roads in and out of Manila, placing humanitarian concerns above military ones except in emergencies. For his part in the capture of Manila, MacArthur was awarded his third Distinguished Service Cross.

After taking Manila, MacArthur installed one of his Filipino friends, Manuel Roxas —who also happened to be one of the few people who knew about the huge sum of money Quezon had given MacArthur in 1942—into a position of power that ensured Roxas was to become the next Filipino president. Roxas had been a leading Japanese collaborator serving in the puppet government of José Laurel, but MacArthur claimed that Roxas had secretly been an American agent all the long. About MacArthur's claim that Roxas was really part of the resistance, Weinberg wrote that "evidence to this effect has yet to surface", and that by favoring the Japanese collaborator Roxas, MacArthur ensured there was no serious effort to address the issue of Filipino collaboration with the Japanese after the war. There was evidence that Roxas used his position of working in the Japanese puppet government to secretly gather intelligence to pass onto guerillas, MacArthur, and his intelligence staff during the occupation period.

One of the major reasons for MacArthur to return to the Philippines was to liberate prisoner-of-war camps and civilian internee camps as well as to relieve the Filipino civilians suffering at the hands of the very brutal Japanese occupiers. MacArthur authorized daring rescue raids at numerous prison camps like Cabanatuan, Los Baños, and Santo Tomas. At Santo Tomas Japanese guards held 200 prisoners hostage, but the U.S. soldiers were able to negotiate safe passage for the Japanese to escape peacefully in exchange for the release of the prisoners.

After the Battle of Manila, MacArthur turned his attention to Yamashita, who had retreated into the mountains of central and northern Luzon. Yamashita chose to fight a defensive campaign, being pushed back slowly by Krueger, and was still holding out at the time the war ended, much to MacArthur's intense annoyance as he had wished to liberate the entire Philippines before the war ended. On 2 September 1945, Yamashita (who had a hard time believing that the Emperor had ordered Japan to sign an armistice) came down from the mountains to surrender with some 100,000 of his men.
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