Faking the Dead - Subverted. The real Atlas went into hiding for so long that Fontaine thought he was dead and stole his identity. Then he shows up again, just in time to watch his family die.
Suicide Not Murder - Inverted. Hester believes that James would have never done such a thing, because he was so happy with her, and his fiancee Mallorie must have had something to do with it... She's wrong.