Digging for the Bones by Paganaidd (джен)

Rather than allowing Harry to stay at Diagon Alley after he blew up Aunt Marge, the Ministry sends Harry back to the Dursleys. Harry returns to school after a terrible summer, to find that he's not the only one with this kind of secret. A student has been killed by his family. New screening measures are put into place by the Ministry: Every student must be given a medical exam and interview to look for child abuse. With Dumbledore facing an inquiry, Snape is entrusted with the task of making sure EVERYONE receives one.
Answer to the "New measures for screening abuse" challenge at Potions and Snitches.
The first chapter contains a character death and the whole story is quite dark. It begins at the beginning of Prisoner of Azkaban and is AU thereafter. Also note: this story is a "Snape is Harry's biological dad" story. This is not supposed to be the central theme of the story, but people have gotten annoyed that I didn't tell them at the beginning.
Another note: There are no pairings in this story, or explicit sexual content. There are, however, mentions of homosexuality. Since there are no pairings, there is no slash content, but if the mere mention of homosexuality offends you, read something else.