Tomonaga’s disappointing battle report placed Nagumo in a quandary. As per Yamamoto’s instructions, he’d held back half of his attack aircraft and the best crews to be ready to strike should the American carriers appear earlier than expected. Yet, now it was clear Midway was still operational, and thus its planes a continuing threat. But the second wave was standing by armed with torpedoes or armor-piercing bombs to deal with ships. To launch a second strike against the island would mean to return the planes below decks and re-arm them with high explosive fragmentation bombs.
Amazingly, Nagumo still had no idea that any American ships were in the area, let alone three carriers just 200 miles to the northeast. So sure was he that there were no hostiles (because nothing had been heard from the submarine pickets by Hawaii) that he opted to launch his strike wave against Midway that morning before sending out just seven scouts on what he thought was a pro forma search. After two hours, his eyes in the sky, as expected, reported nothing to see. But the reconnaissance had in reality been a calamitous failure. One scout plane did, in fact, overfly the zone where Task Force 16 was getting ready to launch, but somehow missed them. Feeling secure that the U.S. Navy was not an immediate threat, and believing it a waste to have half of his attack planes sitting idle waiting to go after an enemy that had yet to materialize while a real threat of land-based enemy aircraft remained, Nagumo ordered his second wave below to re-arm with bombs to finish off Midway’s airfield. It was an arduous process that would take 90 minutes.