Many have suggested he's a part of Ember...?
The principal that is.
But if EMBER is a branch of the government, if it was true why would the Principle say he didn't want the authorities messing with his business? Wouldn't they be allies?
The guy at the mall was also presumably in cahoots with Ember. And malevolent organizations usually have their own agendas even though, ostensibly, they're supposed to be working together.
I think that John spent a year being reeducated, in order to make sure he wouldn't become a danger to society. Once he was ready, he was given a new chance by the authorities. Weather he chose to pass as powerless or not I don't know. The principle though, has his own thing going on. I think he might be in cohorts with the dude at the mall and has some high-tier elitist crazy plan cooking. Or else why make sure that the school's paper frames his own students?