One of Newt's middle names is Artemis, which happens to be the name of the Greek goddess of wild animals and virginity among other things. So give me a story in which Newt, for whatever reason, believes that being a virgin is vitally important to his profession and is the thing that makes his animals bond so closely with him. Sometimes, when he opens up, he ends up being downright sanctimonious about it. Bragging about how he's never even been kissed, and making claims that anyone who has sinful thoughts about him will be struck down (or something idk)...

I can see this going one of two ways:
Light version: Newt's LI helps him sort out his issues and eventually deflowers him. Newt is shocked and relieved to find that his animals still treat him exactly the same, because his virginity is absolutely not what makes them like him.

(LIs in order of preference: Jacob, original Graves, Credence, Tina)

Dark version: Grindelwald (or other bad guy of choice) rapes Newt to sever his connection with his animals. Hopefully that doesn't happen, and they end up comforting him.