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Yes, but the planes themselves were not on the decks - the planes being on the decks is something "everyone knows" that just wasn't so as it was based on what is basically a farrago of lies written by a Japanese author to excuse how 'easily' the Kidō Butai were foiled to the Japanese public. After all, the gaijin were inferior and they should have been defeated easily, right? Well, Western historians copied that crap and now 'everyone knows' it. The Japanese also hadn't left bombs and torpedoes on the flight deck - just like the American carriers, they were arming and fueling aircraft in the hangars. Same kind of thing happened to USS Franklin late in the war, but due to US damage control training, US ship designers using damage control as a primary design principle, and many courageous men, the Franklin made it home. In fact, the above reasons are why a ridiculous number of US ships made it home (or at least floated long enough for the crews to get off in an orderly fashion) with damage that any other navy's ships would have resulted in destruction. The US Navy's absolute obsession with damage control in the interwar period through WW2 paid off in a huge way, though it was quite hard on the crews at times. Funny thing is that we got the idea off the Germans after the Battle of Jutland. They lost the plot, we didn't - and even the Royal Navy, initially thought to be the kings of damage control, was a definite distant second to the US Navy in WW2.