With three of their four carriers blazing furiously by 1030 on 4 June, Hiryu, steaming ahead of the others, was the sole remaining Japanese hope. She responded agressively, launching a strike force of eighteen dive bombers at about 1100 and a second force of ten torpedo planes some two-and-a-half hours later. The bombers hit USS Yorktown at about noon, temporarily stopping her. The others executed a successful torpedo attack on the same ship at about 1445, putting her completely out of action. Though most of the Japanese planes were lost, enough got back to allow Hiryu to prepare a third strike.

Just before Hiryu's bombers came in, Yorktown launched a group of ten SBDs to search for the Japanese carrier, which Rear Admiral Frank Jack Fletcher suspected had survived the morning attack. Two planes, piloted by Lieutenants Samuel Adams and Harlan R. Dickson, spotted Hiryu at about the same time that her torpedo planes hit Yorktown. By about 1600, Rear Admiral Raymond A. Spruance's carriers Enterprise and Yorktown had forty SBDs in the air. These found their target shortly before 1700, just as Hiryu was ready to launch her third attack with five bombers and four torpedo planes, all she had left.

The Enterprise planes (including ten refugees from Yorktown) put at least four bombs into the Japanese carrier, destroying her forward flight deck and setting her afire. Later, several Army B-17s attacked, hitting her only with machine gun bullets.

Hiryu, though incapable of offensive action, kept moving until about midnight, when flames and explosions finally stopped her engines. She was ordered abandoned and then torpedoed to hasten sinking, but remained afloat until about 0900 on 5 June. Soon after daybreak, a plane from the small carrier Hosho, accompanying Admiral Yamamoto's approaching battleship force, found the abandoned ship, photographed her and reported that there were still men on board. The destroyer Tanikaze was sent to investigate, but found nothing. Later in the day, this destroyer was attacked by over fifty U.S. carrier planes and, in a notable feat of shiphandling, escaped. Further to the west, the rest of the once-invincible Japanese fleet was in full retreat.