In this journal entry we find out the "very bad man" is Mr. Von Barron, a leader within the organization at the orphanage. He told the boy that his mother didn't want him and he would take care of him now.
The Midwest Occult & Spectral Society did further research to find out the "very bad man" was actually his father who had an affair with his mother and kept him at the orphanage to cover up the affair so no one would know he slept with one of the caretakers. It wasn't known until years later when a woman who worked at the orphanage spoke up. This lead to many more dark secrets...