Basically, while Harry is ignorant of his past in Spiderman 3, Peter and him get involved in a relationship and Peter decides he has to tell Harry what really happened to his father. It's slash. Don't like, don't read. Flames are ignored, by the way. It's based off the movies, obviously. Enjoy.
A Perfect Life with Harry
Everything had fallen into place. And now, why did Peter have to ruin it?
After Harry had lost parts of his memory, his vendetta against Spiderman and his anger towards Peter, all of his feelings of anger and hate, were replaced with feelings of love. Harry Osborne had admitted to Peter that he was in love with him. And after that, everything changed for the better. Peter realized he had feelings for Harry too. He always had. Mary Jane understood and was forgiving and nice about it, reassuring him they good just be good friends.
So as Peter lay, warm, safe in his lovers arms, why was telling him the truth all he could think about? Why did he feel the need to explain to him what had happened to his father, really. Peter pulled away from the other man's grasp and sat up in bed, reaching for his robe that lay somewhere on the floor. He found it and quietly slipped into it, the cloth snug against his bare body, and headed downstairs for some water.
Peter and Harry had even bought a place together, and were like your average homosexual couple. They scared homophobes, were as cute as ever, and had plenty of sex. But Peter still felt the need to tell Harry, and decided that he would, in the morning.
"Pete?" A weary voice came from the stairs. Peter heard footsteps and Harry stopped at the bottom of the stairs, "What are you doing up?" Harry had not taken the same measures to clothe himself, so he stood, naked, looking tiredly at his boyfriend.
"I couldn't sleep," Peter walked casually over to him, fully awake now.
"I got up for work," Harry explained, without being asked to. "What's bothering you?" He wrapped his arms around Peter, pulling him against his hard muscled chest.
"I need to tell you something," Peter said, "Something you don't remember."
"Alright, what's up?" Harry said, yanking his pajama pants on, which had been lying innocently on the tile by the refrigerator.
"Can you sit down?" Peter asked, pulling out a chair at the kitchen table, and then sitting across from it. Harry obeyed looking at Peter with a confused, and curious, expression. "So, I think I'm just gonna say it. Before you lost your memory, you and me, we weren't friends. You hated me because you thought I killed your father. Because you saw Spiderman laying his corpse on a bed in your house and you later found out that Spiderman and me, well, we're one in the same."
"Wait, Spiderman is you?" Harry asked, kinda slow.
"Yes," Peter said, "See, your father was the Green Goblin, one of the villains that tried to kill me. In one of our fights, he attempted to pierce me with his glider, but I jumped out of the way and it hit him instead. I brought him home because I knew you'd want his body."
"Oh, well why didn't you just explain, when we weren't friends?" Harry asked.
"I tried, but you wouldn't allow me too. And you lost your memory because you came to kill me, and well, accidentally got hurt in the process."
"I'm glad I sat down," Harry said thoughtfully, "So is that all, like there's nothing else to tell me? No secrets?"
"Well, there's the fact that I love you, but that's not much a secret," Peter whispered. Harry smiled.
"Nope, that's not a secret at all."