American carrier aircraft had difficulty locating the target. The strike from "Hornet", led by Commander Stanhope C. Ring, did not fly in the right direction. Air Group Eight's dive bombers missed the Japanese carriers. Torpedo Squadron 8 flew in the correct direction. However, the 10 F4Fs from "Hornet" had run out of fuel and had to crash into the ocean. Waldron's squadron saw the enemy carriers and began attacking at 09:20, followed by Torpedo Squadron 6 (VT-6, from "Enterprise") whose Wildcat fighter escorts also ran low on fuel and had to turn back at 09:40. Without fighter escort, all fifteen TBD Devastators of VT-8 were shot down without being able to do any damage, with Ensign George Gay the only survivor. VT-6 lost 10 of their 14 Devastators, and 10 of "Yorktown's" VT-3's 12 Devastators were shot down with no hits. Part of the problem was the poor performance of the Mark 13 torpedoes. Senior Navy and Bureau of Ordnance officers never asked why six torpedoes, released so close to the Japanese carriers, produced no hits. The Japanese combat air patrol, flying Mitsubishi A6M2 Zeros shot down the unescorted, slow, under-armed TBDs. A few TBDs managed to get close enough to drop their torpedoes and shoot their machine guns at the enemy ships. This made the Japanese carriers to make sharp turns. The TBD Devastator was never again used in combat.
Despite their failure to get any hits, the American torpedo attacks made the Japanese carriers unable to prepare and launch their own strike. They also pulled the Japanese combat air patrol (CAP) out of position. As well, many Zeros ran low on ammunition and fuel. The appearance of a third torpedo plane attack from the southeast by Torpedo Squadron 3 (VT-3 from "Yorktown") at 10:00 made the Japanese CAP fly to the southeast corner of the fleet. Better discipline and using more Zeroes for the CAP might have enabled Nagumo to prevent the damage caused by the coming American attacks.
Three squadrons of SBDs from "Enterprise" and "Yorktown" (VB-6, VS-6 and VB-3, respectively) were approaching from the southwest and northeast. The two squadrons from "Enterprise" were running low on fuel because of the time spent looking for the enemy. However, the squadron commander decided to continue the search. He spotted the Japanese destroyer "Arashi". It was moving to rejoin Nagumo's carriers after having unsuccessfully depth-charged U.S. submarine . Nautilus had earlier unsuccessfully attacked the battleship . Some bombers were lost from lack of fuel before the attack started.
McClusky's decision to continue the search was a great help to the US carrier task force and the forces at Midway. All three American dive-bombers squadrons (VB-6, VS-6 and VB-3) arrived at the right time to attack. Most of the Japanese CAP were looking for the torpedo planes. Armed Japanese strike aircraft filled the hangar decks, fuel hoses lay on the decks and bombs and torpedoes were near the hangars, making the Japanese carriers very at risk of being damaged.
Beginning at 10:22, the two squadrons of "Enterprise"s air group split up and attacked two targets. By accident, both groups attacked the "Kaga". Lieutenant Commander Richard Halsey Best and two other planes headed north to attack "Akagi". Coming under an attack from almost two full squadrons, "Kaga" was hit by four or five bombs, which caused heavy damage and starting fires that could not be put out. One of the bombs landed near the bridge, killing most of the senior officers.
Several minutes later, Best and two planes dove on the "Akagi". Although "Akagi" getting one direct hit (dropped by Lieutenant Commander Best). It struck the deck elevator and went all the way through to the upper hangar deck. It exploded among the armed and fueled aircraft. Another bomb exploded underwater which bent the flight deck and caused rudder damage.
"Yorktown"s VB-3, commanded by Max Leslie, attacked "Sōryū". They got at least three hits and caused a lot of damage. VT-3 targeted "Hiryū", but got no hits.
Within six minutes, "Sōryū" and "Kaga" were on fire. "Akagi" was also seriously damaged. The Japanese hoped that "Akagi" could be saved or towed back to Japan. Eventually, all three carriers were eventually abandoned and sunk.
"Hiryū", the sole surviving Japanese aircraft carrier attacked. "Hiryū"'s first attack consisted of 18 dive bombers and six fighter escorts. They followed the retreating American aircraft and attacked the "Yorktown", hitting her with three bombs, which blew a hole in the deck, put out her boilers, and destroyed several anti-aircraft guns. Despite the damage, repair teams were able to fix the flight deck and fix several boilers in an hour. Twelve Japanese dive bombers and four escorting fighters were lost in this attack.
Approximately one hour later, "Hiryū"'s second attack was made. It consisted of ten torpedo bombers and six escorting A6Ms. The US repair efforts had been so well done that the Japanese assumed she must be a different, undamaged carrier. In the attack, "Yorktown" was struck by two torpedoes; she lost all power and developed a tilt to port, which put her out of action. Admiral Fletcher moved his command staff to the heavy cruiser . Neither of the carriers of Spruance's Task Force 16 was damaged.
News of the two strikes, with the reports each had sunk an American carrier (actually "Yorktown" in both cases), greatly improved morale in the "Kido Butai". Its few surviving aircraft were all recovered aboard "Hiryū" where they were prepared for an attack against what was believed to be the only remaining American carrier.
Late in the afternoon, a "Yorktown" scout aircraft located "Hiryū". "Enterprise" launched a strike of dive bombers (including 10 SBDs from "Yorktown"). Despite "Hiryū" being defended by more than a dozen Zero fighters, the attack by "Enterprise" was successful: four, possibly five bombs hit "Hiryū", leaving her on fire and unable to operate aircraft. ("Hornet"s strike aimed at the escort ships but it did not get any hits.) After hopeless attempts to control the fire, most of the crew remaining on "Hiryū" were taken off the ship. The rest of the fleet continued sailing northeast to catch the American carriers. "Hiryū" stayed afloat for several more hours. She was discovered by an aircraft from the light carrier "Hōshō". This led to hopes she could be saved or towed back to Japan. However, soon after being spotted, "Hiryū" sank. Rear Admiral Yamaguchi chose to go down with his ship, costing Japan her best carrier officer.
As darkness fell, both sides thought about the situation and made plans for action. Admiral Fletcher had to abandon the "Yorktown". He felt he could not command from a cruiser. He gave command to Spruance. Spruance knew the United States had won a great victory, but he was still unsure of what Japanese forces remained. He wanted to protect Midway and his carriers. He followed Nagumo during the day and continued to follow as night fell. Finally, fearing a possible night battle with Japanese ships and believing Yamamoto still intended to invade, Spruance pulled back to the east. He turned back west towards the enemy at midnight. Yamamoto decided to continue the attacks and sent his remaining ships searching eastward for the American carriers. He also sent a cruiser raiding force to bomb the island. The Japanese ships failed to make contact with the Americans due to Spruance's decision to pull back eastward, and Yamamoto ordered a withdrawal to the west.
Spruance failed to regain contact with Yamamoto's forces on 5 June even though he made many searches. Towards the end of the day he launched an attack on any ships from Nagumo's carrier force. This strike missed Yamamoto's main group of ships. It did not hit a Japanese destroyer. The strike planes returned to the carriers after nightfall. Spruance to ordered "Enterprise" and "Hornet" to turn on their lights to aid the landings.