A few comments:

-Do we really need huge blocks of the badfic quoted in there? Parts of this verge on MSTing, which is a wonderful art, but not what PPC missions are about.

-Your agents have a nasty habit of not speaking like people (of any species). A random example:

“Voldemort never once transformed into an animal,” he said angrily. “The whole deal about the snake he has on him is because he has a pet snake. And as for proper Animagi, it takes at least a month to prepare for such a transformation! You can’t just get magical powers and a new form in an instant!”

That's an infodump right there. And your mission is fairly liberally littered with them. You don't have to demonstrate that you know every little thing that's wrong with the story, y'know. And... people don't talk like that.

-Talking heads. No, your agents aren't quite literally talking heads - but they really don't feel like they're in the same room as the characters. Go check out a Jay and Acacia mission or two - they spend all their time hiding behind things, straining to hear, etc etc. Your agents are facing basilisks, but seem to be wandering around in the open.

-And... you know how there are some missions you want to reread, because you love the way the agents interact? This just... doesn't do that. Other than canon knowledge, I didn't see anything to really distinguish the agents from each other, let alone from other agents. They were just... two snarky infodumpers hanging around in plain sight.

That's the criticism, I guess. Here's the constructive:

-Go write out what defines your agents. Pick out the things that make them different from each other. Work out ways to integrate those into your missions.

-Give yourself a tight limit for badfic line-usage. One sentence per page? Ten sentences total? It's up to you, but it would be a serious improvement. I'm here to read your writing, not some which you've acknowledged is bad.

-Assume that everyone will notice your agents if they get in their line of sight or make a loud noise. Figure out where your team needs to hide. Give the canons and badfic characters reactions when your agents inevitable start yelling. Dumbledore isn't going to ignore someone ranting in the corner of his office!

Okay, that's enough of that. I think your agents are excellent in concept (though I do have a weakness for maniraptorans, so y'know); I think there's a lot you could explore with them. I also think it's great that you're actually writing missions, which is more than I can say for most people (eg, me!). But I also think that your missions could be much tighter, cleaner, and more engaging.

hS

"Oh, and by the way, the Basilisk is born from a rooster’s egg hatched by a toad."
I don't think roosters lay eggs.

Ripper suddenly felt something on his leg, and looked down to see a spider with a body as big as a man’s fist crawling upon his pants. Startled, the disguised Deinonychus kicked his leg and sent Gryphandor the mini-Acromantula tumbling to the floor.
Only fist-sized? I don’t remember whether Meir Brin told the actual size of mini-Aragogs or left this to the readers imagination, but I do remember that they drag fangirls around at the "Hogwarts Fanfiction Academy" and use them as yoyos. Even if they are surprisingly strong for their size, I cannot imagine fist-sized spiders doing this. (And the mental image of a Hobbit-sized Acromantula trying to scuttle up Ripper’s leg is hilariously creepy.)

The agents exchanged glances. The mini-Acromantula inside Ripper’s bag clicked its sharp pincers. (page 9)
I don’t question whether Gryphandor fits in there and when and how he got in...
The C-CAD started to smolder again. The mini-Acromantula hissed at the scent of smoke, and Ripper hastily shoved the device back into his bag. (page 10)
... but wait, isn’t Gryphandor in there? And when did he get out again?
Ripper nodded in agreement, and followed the disguised Skarmory through the next portal – but not before letting the mini into his bag for safe-keeping. (page 11)
Looks like a continuity error to me.

And there’s a typo:
"For all of these crimes, plus a few more than we cannot care less about, you are sentenced to die, " Ripper finished.
"than" should be "that".

HG