Despite sinking three aircraft carriers and damaging one, Vice Admiral Ozawa of the Second Fleet remained relentless in expanding the achievements in battle.
Although suffering significant losses, the response to the still-operational Midway base was assigned to the Third Fleet. The Third Fleet, after enduring concentrated attacks from US carrier aircraft, had all four of its core aircraft carriers sustain varying degrees of damage. Especially, the Zuikaku had her front elevator pierced by a 1.000-pound bomb, causing chaos in the hangar. Naturally, this made aircraft operations on the carrier impossible, and the planes were dispersed and temporarily moved to the rear on other carriers. On the other hand, despite the damage, the Shōkaku, capable of launching and recovering aircraft even after being hit, along with the slightly damaged Mizuho and Nisshin, maintained their ability to launch and recover aircraft, enabling them to continue the fight. With these three carriers, it was entirely possible to further damage the weakened functions of the Midway base.
Due to this, Ozawa could concentrate on the American fleet's attacks. Initially, usable aircraft returning from the first attack group was organized into the second attack group. Out of the 72 available D3As and B5Ns, many suffered damage, and only 46 were immediately usable—21 dive bombers and 25 torpedo bombers. This was initially less than a third of the original force, showcasing the formidable nature of the American carrier task force's anti-aircraft firepower. Some staff expressed concerns that even with a small number of aircraft, attacking the enemy fleet would result in significant damage and minimal success. Nevertheless, Ozawa's determination to pursue the enemy remained unshaken, and the second attack group was dispatched. In addition to the 46 D3As and B5Ns, each carrier launched a squadron of 12 Zero fighters for added security.
The second attack group, setting out with a sense of unease, found the American carrier task force significantly weakened by the first attack. Therefore, the second attack group managed to suffer less damage than the first and delivered additional blows to enemy cruisers and destroyers. They even succeeded in delivering the final blow to the damaged carrier Saratoga, which was attempting to withdraw from the battle.
In the end, the two air attacks on that day resulted in the sinking of all carriers in Task Force 16 and Task Force 17, with two out of eight cruisers sunk and six suffering damage ranging from moderate to severe. Two surviving cruisers were unable to navigate on their own and were currently being towed by accompanying ships. Out of the 24 destroyers that were present before the battle, only 21 remained, and of those, only six were undamaged, while the remaining 15 had some form of hindrance to their navigation.
At this point, surface strike forces extracted from the Second and Third Fleets launched a pursuit. The four heavy cruisers of the 6th Cruiser Division, Myōkō and Haguro, and the 7th Carrier Division, Ashigara and Nachi, were the main force. The four Asashio-class destroyers, including Asagumo, Yamagumo, Natsugumo, and Minegumo, and the Kagerō-class destroyers Kuroshio, Oyashio, Hayashio and Natsushio followed the heavy cruisers as escorts.
Although the numerical superiority was on the Americans' side, the majority of their ships had suffered serious damage from Japanese carrier aircraft attacks. Apart from the heavy cruisers Northampton and Chester, which were towing companion ships, the only ships capable of moving properly were the two undamaged heavy cruisers, Louisville and Chicago, along with six destroyers. Realizing they could not escape from the Japanese surface strike force relentlessly pursuing them, the Northampton and Chester temporarily suspended towing operations, forming a defensive line alongside the Louisville, Chicago, and six destroyers.
The remaining American fleet had rescued crew members from sinking carriers on all their ships' decks. Among them were a few surviving aircrew and valuable personnel such as weapons officers and flight deck crew, whose numbers were extremely limited. If the remaining fleet were to be annihilated at this moment, it would mean a depletion of the essential personnel needed for the reconstruction of the carrier task force.
The US Navy had already lost tens of thousands of trained personnel in the Battle of Wake Island. Further human losses would jeopardize the very existence of the US Navy organization itself. Therefore, it was imperative for all ships to survive and return to Pearl Harbor at all costs.