The entire series is based on a predestination paradox fighting a grandfather paradox. You could easily argue that every single movie and the tv show all take place in alternate realities. I personally like that about it because it allows them to continually reset and change things up because, arguably, the original future is still happening and every Kyle Reese and T-800 they send back just makes an alternate timeline. I will admit though, having an Indoctrinated John is taking things direct to crazy town.
