At 02:15 on the night of 5/6 June, Commander John Murphy's , in the water west of Midway, made the second of the submarine force's major contributions to the battle's outcome. Sighting several ships, neither Murphy nor his executive officer, Ray Spruance, Jr., could identify them. Considering that they might be US ships, Murphy did not fire, but reported the ships to Admiral Robert English, Commander, Submarine Force, Pacific Fleet (COMSUBPAC). This report was sent to Nimitz, who then sent it to Spruance. Spruance assumed this was the invasion force and moved to block it while staying northeast of Midway.
The ships sighted by "Tambor" were the four cruisers and two destroyers Yamamoto had sent to bomb Midway. At 02:55 these ships received Yamamoto's order to pull back and changed course. At about the same time as the course change, "Tambor" was sighted, and to avoid a submarine attack and hit into each other, causing serious damage to "Mogami"s bow. The less severely damaged "Mikuma" slowed to . This was the most damage any of the 18 submarines deployed for the battle achieved. Only at 04:12 did the sky brighten enough for Murphy to be certain the ships were Japanese, by which time staying surfaced was hazardous, and he dived to approach for an attack. The attack was unsuccessful, and at around 06:00 he finally reported two westbound "Mogami"-class cruisers.
Over the following two days, first Midway and then Spruance's carriers launched several attacks. "Mikuma" was sunk by Dauntlesses, while "Mogami" survived damage and returned home for repairs. The destroyers "Arashio" and "Asashio" were also bombed and machine-gunned during the last of these attacks.
The "Yorktown" was towed by USS "Vireo". In the late afternoon of 6 June, however, fired torpedoes; two struck "Yorktown", but a third struck and sank destroyer , which had been providing power to "Yorktown". "Hammann" broke in two with the loss of 80 lives. "Yorktown" sank just after 05:00 on 7 June.
By the time the battle ended, 3,057 Japanese had died. Casualties aboard the four carriers were:
"Akagi": 267; "Kaga": 811; "Hiryu": 392; "Soryu": 711; a total of 2,181. The heavy cruisers "Mikuma" (sunk; 700 casualties) and "Mogami" (badly damaged; 92) accounted for another 792 deaths.
In addition, the destroyers "Arashio" (bombed; 35) and "Asashio" (strafed by aircraft; 21) were both damaged during the air attacks which sank "Mikuma" and caused further damage to "Mogami". Floatplanes were lost from the cruisers "Chikuma" (3) and "Tone" (2). Dead aboard the destroyers "Tanikaze" (11), "Arashi" (1), "Kazagumo" (1) and the fleet oiler "Akebono Maru" (10) made up the remaining 23 casualties.
After winning a victory, and as pursuing the Japanese ships became too dangerous near Wake, The American forces pulled back. Spruance pulled back to the east to refuel his destroyers and meet with the carrier "Saratoga", which was carrying replacement aircraft. The American carriers eventually returned to Pearl Harbor. Historian Samuel E. Morison wrote in 1949 that Spruance was criticized for not pursuing the retreating Japanese, allowing their fleet to escape. Clay Blair argued in 1975 that had Spruance followed Yamamoto, he would have been unable to launch his aircraft after nightfall, and his cruiser escorts would have been destroyed by Yamamoto's larger and more powerful ships, including the battleship , with 18-inch guns.
On 10 June, the Japanese Navy gave an account of the results of the battle that did not tell the whole story. Nagumo's battle report was given to the high command on 15 June. It was intended only for the highest officers in the Japanese Navy and government. It was guarded closely throughout the war. Nagumo stated that the enemy was not aware of our plans. The Japanese public, and much of the military, were not told about the defeat: Japanese news announced a great victory. Only Emperor Hirohito and the highest Navy officers were told about the carrier and pilot losses. Army planners continued to believe that the fleet was in good condition.
On the return of the Japanese fleet to Hashirajima on 14 June the wounded were transferred to naval hospitals. Most were called "secret patients" and kept away from other patients and their families. The Navy did this to keep this major defeat secret. The remaining officers and men were quickly spread out to other units of the fleet and sent to the South Pacific, where the majority were killed. None of the flag officers or staff of the Combined Fleet was penalized, with Nagumo later being placed in command of the rebuilt carrier force.
The Japanese Navy learned some lessons from Midway. Aircraft were refueled and re-armed on the flight deck, rather than in the hangars. All unused fuel lines were drained. The new carriers being built with only two flight deck elevators and new firefighting equipment. More carrier crew members were trained in damage-control and firefighting techniques. The losses later in the war of , ', and ' showed that there were still problems in this area. Replacement pilots went through a short training program, meeting the short-term needs of the fleet. This led to a decline in the quality of training. These inexperienced pilots were sent into front-line units, while the veterans who remained after Midway and the Solomons campaign were kept flying continually. As a result, Japanese naval air groups declined in quality during the war.
Three U.S. airmen, Ensign Wesley Osmus (pilot, "Yorktown"), Ensign Frank O'Flaherty (pilot, "Enterprise") and Aviation Machinist's Mate B. F. (or B. P.) Bruno Gaido (radioman-gunner of O'Flaherty's SBD) were captured by the Japanese during the battle. Osmus was held on the "Arashi", with O'Flaherty and Gaido on the cruiser "Nagara" (or destroyer "Makigumo", sources vary), and later killed. O'Flaherty and Gaido were tied to five-gallon kerosene cans filled with water and dumped overboard several days after the battle.
The Battle of Midway has been called "the turning point of the Pacific". However, even after Midway, the Japanese continued to try to get more territory in the South Pacific. The U.S. did not become the more powerful navy until after several more months of hard combat. Midway was the Allies' first major victory against the Japanese.
However, it did not change the course of the war by itself. It was the combined effects of the battles of the Coral Sea and Midway that reduced Japan's ability to do major attacks. In addition Midway helped make US landings on Guadalcanal possible. The prolonged attrition warfare (a type of battle in which each side tries to wear down the other side) of the Solomon Islands campaign allowed the Allies to take an offensive stance for the rest of the Pacific War. Finally, Midway bought the United States time until the first of the new Essex-class fleet carriers became available at the end of 1942.
The battle also showed the worth of pre-war naval code breaking and intelligence-gathering. These efforts continued in both the Pacific and Atlantic areas of war. There were many successes. Navy code breaking made possible the shooting down of Admiral Yamamoto's airplane.