one girl had the problem of being too beautiful, inside and out, and the ensuing popularity with men and jealousy from women practically ruined her life. Upon transferring to the MC's school the MC, being the average guy that he is, sees her as being massively beyond his league and doesn't really pay attention to her much. All the other guys on the other hand just can't get enough of the girl, and the girl sees the MC as being the one guy different from all the rest, someone she can bond with and trust not to go gaga on her (despite the fact he kinda does but just acts realistic about it). One thing leads to another and MC and girl become secret close friends and then slowly becoming more intimate as chapters go along. It doesn't even take long for the girl to confess attraction to the MC, because of what he initially provides her - companionship without having to worry about her looks and such. It also helps that our MC has an amazingly large penis, yes thats a thing.
She's raped and on the brink of death, saved only by the rather late arrival of the protag. She pratically dies as he f*cks her for dear life and transforms into a partially brain-dead golem but slowly regains her personality and memories as the story goes along.