The line about someone controlling Mega Man's every thought and action is an allusion to a gag from "The Lost Vikings", a great if somewhat underrated video game for the SNES. As I think I've mentioned before, at the end of each level of that game, the three characters banter a bit before moving on to the next level. At the end of one particular level, Olaf (the Stout) asks Erik (the Swift) and Baleog (the Fierce) if they ever wonder if there's someone "out there", controlling their every movement and action. Erik and Baleog tell him he's just being paranoid, but then he points to the player and demands to know who that is. They all freak out and run away. I always loved that little bit of fourth-wall breaking in the game, and it more or less inspired this comic... hell, it basically inspired this entire storyline.
Anyway, as far as the comic goes, though, I like to think that while there technically is someone controlling the characters' every thought and action, the characters have personalities of their own and have been known to act independently based on those personalities. I would often find myself surprised at little twists and turns in the comic brought about not necessarily by my own preordained plans, but by the characters involved and what they wanted to do. Which probably means I'm crazy.
On a different note, I'm not entirely sure why the Author's flying here, but if I had Author powers, I would.