I prefer pre-slash Graves/Newt or just friends Jacob & Newt. Anyway, the other (for Nefarious Reasons) was forced to rape Newt. After, Newt Obliviates the other. Because he can deal with it having been done to him, but knows the other can't deal with having done it.

Filler can write the rape, but I'm more interested in the angsty aftermath with the other vaguely remembering and feeling haunted. And Newt having to remind himself that the other had no choice (and maybe he's not dealing as well as he thought). And of course, eventual hurt/comfort.