— Sarah to Ellison in Mr Ferguson is Ill Today.
Sarah is the wizard and she's trying desperately to get Dorothy (John) home again (a normal life).
I've always assumed future!John was the man behind the curtain because he's pulling the strings from the future. But that line from Mr Ferguson has been stuck in my mind ever since that episode. With all the Wizard of Oz references, that couldn't possibly just be a throw-away line. It has meaning. And before that, in Goodbye to All That, we had Sarah reading the Wizard of Oz and (I think) coming to the realization that John is essentially Dorothy. Until the wicked witch is dead — until his fate is changed, he can never truly be free to live his life.
So even while future!John is the one sending back missions (messages to his mom from the future), it's Sarah who's in the position to actually change things. She's the one who has the power to alter the future and everything she does either gets John a step closer to his fate or a step closer to "home".