Moral Event Horizon: If Atlas using Julia and lying to her in order to create a Philosophers Stone isn't bad enough, then there's him murdering her parents and stealing her brothers face when they were both still children, whom he was supposed to be protecting.
The Untwist: It is pretty obvious that Atlas is the fake Ashleigh and Herschel is the real Ashleigh, Its noticeable when Atlas has a scar that looks like he is stealing a face and Herschel having no facial skin under his mask.
What Do You Mean, It's Not Political?: People from Milos trying to reach Table City are shot down, and the whole issue of deporting illegal immigrants and the fact that most people from Milos (at least the ones whom name we know) are named with Mexican-sounding names, like Carlos, Santos, Julia, Miranda, Raúl, Anita, Pedro and Gonzalez. Not to mention the flashback scenes of the people of Table City being conquered by one people, then another, both times being conscripted into the defender's army to try and stop them.