While MacArthur was planning a round-about, island-hopping route to Japan by way of the Philippines, Nimitz wanted to advance more much directly on the Japanese Home Islands, across the wide, open waters of the central Pacific. But this plan would require a huge fleet of aircraft carriers to overcome Japanese shore-based aircraft. While this carrier fleet was being built, most of the visible fighting would be limited to pin-prick raids for morale-building purposes (like the Doolittle Raid on Tokyo or Carson's Raiders' landing on Marcus Island) or to defensive battles (the Coral Sea, Midway and Guadalcanal). MacArthur, on the other hand, could start his plan immediately, under the cover of defending New Guinea, which led to the Pacific War being fought according to two conflicting, unapproved plans, and gave his Army rival a head start.
But Nimitz had already started the secret campaign that would end by bringing the Japanese Empire to its knees, before either MacArthur's or Nimitz' intended master plans had delivered a single Marine to Tokyo! Shortly after taking command, Nimitz made the key decision: He would employ his submarines in "unrestricted warfare" against the Japanese merchant fleet, rather than as just a scouting force for the fleet. Pre-war plans had all emphasized the latter mission and avoided the idea that our submarines would ever imitate German U-boats, by attacking defenseless merchant vessels. But the battleships that were supposed to carry the war to Japan in those plans were now on the bottom of Pearl Harbor and his few carriers were too valuable to risk in more than one raid on the Japanese Home islands. His subs, however, had the range to reach Japan and the stealth to survive in enemy home waters. Attacking merchant vessels would not be as dramatic as sinking enemy warships, but it might serve to distract the Japanese and slow down their offensive.
Even though it was recognized that Japan might be even more vulnerable to submarines than Britain had been in World War I (which U-boats had once seemed close to winning) few people expected that our subs would have a decisive effect. Improvements in anti-submarine warfare weapons since 1918 had convinced most naval officers that the sub was not going to be very effective in the next war. U-boat successes since 1939 were not obvious in 1941, as U.S. observers did not know then how many ships the Allies had lost, nor how few U-boats had been needed to sink them.
Initially, the doubters seemed to be right. The results were not merely unimpressive, they were tragic. U.S. submarines were hampered by over-cautious commanders, better trained to avoid peacetime accidents than to close with the enemy. Many of the subs were temperamental, experimental designs, plagued with engine breakdowns. Worst of all, the standard torpedoes were so badly designed that it was possible to score fourteen consecutive hits and have none of them explode! In spite of heavy U.S. losses (one fourth of all U.S. Navy subs were lost in the war, most of these in the early years) the Japanese did not seem to be hurting badly.
But Nimitz did not give up on subs. By mid 1943 peacetime tactics and leaders were gone, the U.S. had replaced its aging submarine prototypes with new, highly reliable "fleet boats", and the many defects of their torpedoes were fixed at last.
Meanwhile, the Japanese had responded only slowly to the rather ineffective submarine threat they had seen so far. Japanese submarines continued to operate only against major allied warships; attacking a merchant ship gave away your position. The submarine was there to scout for the fleet, or ambush a carrier, cruiser, or battleship, if possible, but not to waste torpedoes! Their antisubmarine warfare equipment and tactics had not been massively improved like those of the Allies, and they still regarded protecting the merchant fleet as an inferior duty for obsolete ships.
Thus, just as the Allies were triumphing over the U-boats in the Battle of the Atlantic, in mid 1943, the U.S. submarine war in the Pacific went into high gear. Japanese shipyards had not been able to replace even the modest losses they taken so far, and the merchant ships available were already barely adequate to maintain the flow of raw materials and food that Japan needed. The increased losses in the next two years were so devastating that Japan was literally unable to feed itself, let alone operate its war industries at capacity, by 1945. In the end, U.S. subs not only destroyed the transports Japan needed to survive, they also sunk a greater tonnage of Japanese warships than carrier aviation, land-based aircraft, surface warships, or any other allied forces.
When the dropping of the two atomic bombs brought the war with Japan to a sudden end, it had already been won by Nimitz' submarines.