The story is about a high schooler(Guy 1) living with this man (Guy 2) whose probably a tutor or teacher. In Guy 2's high school years, he was a delinquet, the complete opposite of his present-self. He would have sex with classmates, teachers, etc. to pass time, bribe teachers, etc. Guy 2 fell in love with a teacher, which is Guy 1's father who eventually brought him on the right track. After the father passed away, Guy 1 eventually was in Guy 2's care. (Present time) Guy 1 expresses his love constantly to Guy 2 despite being rejected all the time, in the end they get together any way.

Scene 1 (that I remembered): Guy 1 was in search to find condoms when finds a box of things in the past from his father. Inside, he finds a letter from Guy 2 written when he was in high school; he expressed the love he had towards his father.

Hope my description is detailed enough, even though there's probably billions of manga stories like this.

Um...this probably should have been put under the yaoi section...

Either way, I'm pretty sure it's Oni ni Hatsujou

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Tesla: If an immortal vampire dies in a virtual world-

Magnus: -does he make a sound?
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Likes: Action, adventure, drama, fantasy, historical, horror, mystery, psychological, sci-fi, seinen, shounen, supernatural, tragedy

...I read too much >.>

Oni ni Hatsujou, no doubt about it.