without knowing more of the story it is hard to know what to say. my first response is that he was playing mind games with you to tell you that you raped him after three years, you say you were horrified at being told this, but you don't go into any detail as to whether his claims were valid. could he have been manipulating you into believing this for some reason?

regardless, I hope that you are in counseling as this situation, which you clearly didn't intend, has devastated your life and it is going to take much working thru to fix it. make sure to get someone who specializes in sexual trauma if you really want therapy to work,