Knowing Timelord biology (or at least the fact that it's messed up) I'm not entirely sure of the Neuralyzer would even work on him. Then again, he'd probably understand the PPC and everything else, so he'd either pretend to not remember or just come to an agreement not to mention it again.

Heck, I can imagine that.
"Hey, Doctor, look at the-"
"Yes, the pretty lights. I know."

is pretty damn stupid. He'd fall for the neuralyzer trick. If he had been written in character he'd probably figure it out, but if he were written in character there probably wouldn't be any agents in the story in the first place.

Speaking as a fairly new Doctor Who fan, I'd have to say the Doctor would be the best possible canon character to fall through, and also the worst, and it would be awesome to see this written.

I'm torn-- part of me thinks it would make perfect sense for the Doctor to look away from the pretty lights and bluff the Agents into thinking he'd been neuralysed-- but then he'd probably not bother going back. HQ does qualify as a parallel universe, right? As canons are all spots in the multiverse? So being in HQ-- or another canon-- would render the TARDIS powerless, and being a man Time Lord of brilliance, he'd probably just go on about his way. A love of getting into trouble probably would be trumped by a desire to not destroy the multiverse. *shrug*

Then again, part of me thinks he'd just go on his merry way, and that largely because it would be so awesome to see the Doctor rampant in HQ. But yeah.

(Also, I believe canon characters have made it into HQ before. They're generally extracted and neuralysed, eventually.)

For a start, the PPC are very very careful not to leave tech in any canon.

For another thing, when PPC tech breaks, it tends to break very spectacularly and often either melt or explode. This is for comedy. We like comedy.

And lastly, well, we *really* do like comedy, and doomsday scenarios aren't very comic. Let's not get too serious, eh? :D

There are characters in various fandoms that have knowledge of or are able to see PPC Agents. Elrond from LoTR, Jack Harkness from Torchwood, and Death from Discworld spring to mind. Death at the very least appears to be immune to neralyzation (although he is a good sport about it and allows it to happen anyway) and there haven't been any problems associated with this so far.

Falling into a plothole is usually just the result of the badfic author forgetting about the character, or shoving them out of the way when a replacement comes. Plotholes act more like sinkholes in that way - one entrance, no exists, like a little bubble of reality. The portals agents use are generated using plotholes, but aren't plotholes in themslves. And, even if plotholes were to act like wormholes, there's no reason any of them would lead to the PPC - after all, no badfic author writes us into their stories. Besides, we take canons into HQ all the time for medical purposes, the Doctor included.

So don't worry, your armageddeon is so far from likely as to be more or less impossible. :)

We put bells around all their necks. /kidding

You're right! One misplaced DORKS and the entire continuum could disintigrate. Oh man this could be bad. Even though there is the Very Important Rule of not leaving anything behind, this could be catastrophic if say a newbie left one behind on accident.