Like, they are the best of friends but because they are so different, even the classes they take are not the same. Thus, even once they graduate, he believes her to be a guy.
Then, they meet up again in the business place. She...unfortunately still lacks a feminine body and the MC still thinks of her as a dude. But, now that she is more mature, she likes how close he is. It's honest, right? She knows how he truly thinks but doesn't tell him anything.
So, after a get-together with coworkers, she gets him drunk and sleeps with him, but MC was too shitfaced to know so the next day he just freaks out and runs away. And now he has to live with these weird feelings for who he thought was a guy and is it gay or not that kind of thing.
And so the girl never tells him, just getting closer and more aggressive. Eventually, by the time he decides there is no point in fighting his feelings, she comes clean. And then the confusion sets in again.
Sounds like a Korean drama or something. I also think I've read that scenario in a Japanese manga before. It was good, though I didn't finish it or it was dropped/axed.
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