Why did tje pilot suddenly start crying before offering Jim a mango

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Because his plane wouldn't work and he couldn't go on his mission, and meanwhile Japan lost the war and there's nothing more he can do now, so he basically feels he's a failure and has to go home in disgrace.

He felt guilty because he was becoming friend with the "enemy" who just won the war against them.

Most likely he was crying from being dishonourable to his country. They were kamikaze pilots stationed there and he was still alive.