MacArthur was the General of the Pacific fleet Navy during WWII. He led a southern attack against Japan that began just above Australia and eventually captured every Japanese occupied islands except the mainland.

According to B. H. Liddell Hart's History of the Second World War (Da Capo Press paperback edition 1971, Page 346) "At the beginning of April (1942) the United States had assumed responsibility for the whole Pacific area, except Sumatra, While the British would remain responsible for Sumatra and the Indian Ocean area." ... The Americam sphere was divided in two -- the South-west Pacific under General MacArthur, whose headquarters were now established in Australia and the Pacific Ocean area under Admiral Chester W. Nimitz. Both were strong abd forceful men, likely to clash. The Japanese plan provided ample call on, and scope for, the activity of each. Moreover the borderline between their respective spheres came in the Solomon Islands, where the Japanese amphibious threat required the conjoint use of MacArthur's ground forces and Nimitz's naval forces."

As this quote indicates, MacArthur was not General of the Pacific fleet. He was an Army officer commanding the U.S. ground and non-naval air forces primarily responsible for the destruction of Japanese ground forces scattered on the many Pacific island locations. Whether all of these were captured by the General is best discussed under a topic directly related to that aspect of the war including those islands initially bypassed. The U.S. Paciific fleet including its naval aviation forces (as well as coordination with the British Pacific fleet) were under the overall command of Admiral Chester Nimitz.

At the outset of the War, MacAurther was in command of the US forces in the Philippines. During the initial attack, he was responsible for organized resistance there. When the situation in the became tactically hopeless, he was ordered to escape to Australia by President Roosevelt. His arrival in Australia allowed him to rally the rather demoralized Allied forces in the area, as he quickly assumed command of all local Allied forces in the area.

For mostly political considerations, the Allied war effort in the Pacific was actually divided into three major theaters: the Southwest Pacific Area, the Pacific Ocean Areas, and the Southeast Pacific Area. MacAurther (and, by inference, the Army) was assigned to coordinate all Allied forces in the Southwest theater - this included not just army, but also all naval forces and air forces in that area. Fundamentally, this left MacAurther responsible for the defense of Australia, and any action in the Indonesian/Malaysian archipelago down to New Guinea and up to the Philippines.

MacArthur commanded a very mixed group of forces, consisting primarily of American, Australian, and British, but also Dutch, Free French, and several indigenous nationalist groups. For the vast majority of the war, the fighting consisted mostly of smaller (but no less intense) land and naval actions, primarily defensive on the part of the Allies. The retaking of the Philippines was the major exception to this, with the overall command of the operation falling to MacArthur.

He was present at, and signed for the United States, the formal surrender of Japan on board the U.S.S. Missouri on 2 Sept 1945.
US general who served as chief and commanded the Allied forces in the South Pacific during WW2