With her boiler rooms out of action through the effects of the bomb hit in her uptakes, Yorktown coasted to a stop, while her escorts circled around her. Her crewmen fought fires in her smokestack and elsewhere, patched holes in her uptakes and flight deck, treated casualties and stayed alert for another possible enemy attack. The crew of one boiler room heroically worked amid heat and smoke to keep the ship's auxiliary systems operating.

To maintain his mobility, Task Force 17 commander Rear Admiral Frank Jack Fletcher shifted his flag to USS Astoria. Ships were sent from the nearby Task Force 16 to reinforce those clustered around the stricken carrier. Meanwhile, Yorktown aircraft returning from attacks on the Japanese carrier Soryu were diverted to USS Enterprise. Some, however, were too short of fuel to fly on, and ditched nearby.

As damage control parties made progress, flight deck crews respotted several fighters aft to takeoff position and the engineering force began to bring other boilers back into service. After nearly two hours' hard work by all hands, Yorktown was underway again, though only capable of about twenty knots speed. To the west, as yet undetected, Japanese torpedo planes from Hiryu were approaching.