Midway's results are really quite complicated, thanks to a combination of pressure, doctrine, operational and tactical ongoings and outright luck.
TLDR
1 - Prior to sailing, Nagumo was ordered to keep 50% of his aircraft available for an anti-shipping strike should the USN carriers be found.
2 - This meant that in reality the strike against Midway was pretty much guarenteed NOT to knock it out so a 2nd strike WOULD be needed.
3 - Recon planes found nothing. So without a threat in the area Nagumo ordered his reserve to be rearmed with bombs.
4 - Whilst all this is going on the IJN carriers were coming under repeated attacks from Midways aircraft (dive bombers, twin engine bombers, torpedo bombers and B-17s)
5 - Then the USN's carriers started getting involved as well
6 - Its at this point that IJN recon spots the US ships, initially beliving them to be a surface action group, no CV was spotted.
7 - Nagumo hesitates and keeps his aircraft being armed with bombs for Midway, after all, cruisers and DDs are no match for his force.
8 - A WILD YORKTOWN CLASS CV APPEARS!
9 - Nagumo orders the aircraft being bombed up to halt arming ops and to be re-armed with anti-ship bombs and torps.
10 - All the land attack ordanace is left on the hangar decks (it simply takes too long to move it down into the magazines)
11 - USN attacks are ongoing with heavy losses for no gain, but the pressure is stopping the IJN from getting into any operating tempo other than constantly launching CAP fighters.
12 - Midway strike planes land and this halts any flight deck operations as the aircraft are brought down to be re-armed and refueled.
13 - Nemesis arrives when divebombers from the Yorktown and Enterprise make their attacks. IJN hangers are mostly full of planes being bombed up, or refuelled or ready to be brought up to the flight deck to be spotted.
14 - Boom.
The IJN also did have weak damage control parties, unlike the USN where pretty much everyone was trained how to fight fires or deal with flooding. On the IJN it was down to specific teams of men and their officers (who did a lot more than the USN and were basically the equivalent of a senior seaman in USN terms).
Really if you want a good book about Midway, read Shattered Sword its pretty much the definitive book on Midway and how it all went wrong.