The researcher's letter is found in the sidequest Research Project, after going to Emil's Mansion and then going to Seafront. It gives a bit more background information about Emil.
Letter
Dearest Emil,
You do not know me, but I know you. My research has twisted your life in unfathomable ways. I tried to make up for this by serving as your mother, but I know now that my efforts fell far short. I would have done anything to save you from this fate, and you will never know how guilty I feel that I could not.