Following the 4 June attack on Midway's facilities and the day's great battles between opposing aircraft carrier forces, the Japanese briefly considered continuing their campaign. However, as the full extent of their disaster became clear, they began a general retreat. After a brief withdrawal to avoid the risk of a night action, the two remaining U.S. carriers pursued the enemy forces, unsuccessfully attacking a destroyer on the 5th.

On 6 June, U.S. planes found and attacked two Japanese cruisers, sinking the Mikuma. Meanwhile, USS Yorktown had remained afloat. A salvage party returned to try to save her, but this effort was thwarted on the afternoon of the 6th, when a Japanese submarine found and torpedoed the carrier and the accompanying destroyer Hammann. The battered, gallant Yorktown sank the following morning.

As Battle of Midway combat activities gradually wound down, PBY patrol seaplanes and ships busied themselves rescuing downed aviators, the last of whom was recovered on 21 June. A U.S. submarine found two Mikuma survivors, and 35 of Hiryu's crewmen were picked up on 19 June. Earlier, men from Yorktown and Hammann had been taken to Pearl Harbor, where reinforcements were being forwarded to Midway and the nearby carriers. USS Saratoga (CV-3) arrived from the west coast on 6 June with a full load of aircraft. She quickly returned to sea, en route to join Enterprise and Hornet. Later in the month, fresh Marines were landed at Midway, which remained an important U.S. base for the rest of World War II, and beyond.