Here's my best guess about what is going (I just thought of this about 10 minutes ago, and for all I know, it's been realized by other viewers, already) ... but -
I think all of John from Cincinnati - everything that we're seeing in Imperial Beach - is taking place in a virtual, Matrix-like world.
That's why John (and in the last episode, John and Shaun) have nothing to say about where they were when they were gone from IB.
That's how John was able to bring Shaun back from the dead or near-dead - the player outside the virtual world made that happen. Same with the levitation, etc - all the things that seem unreal to us are games the game-player is playing in his/her control of the virtual world.
Possibly the Howard Hesseman character - the chemist - is the creator, designer, or just player of this game - and that's why Mitch went to him. Or maybe it's Linc. Or - hey - could be Dwayne with his computers.
In any case, it would explain why so much of John's powers are on screens, why Linc gave the rant about the Internet, etc... (It might also explain the dead-guy in the motel.)
I give this theory about a two-percent chance of being right (I read yesterday in the New York Times that some philosophy dudes think there's a 20-percent chance that all of us are in a virtual reality sim - I have no idea how one could come up with any percentage of probability for this.)
So, there you have it - have at it...
The Plot to Save Socrates
"a Da Vinci-esque thriller" - New York Daily News
"Sierra Waters is sexy as hell" - curled up with a good book