I like how he explained those funny leg-things.

Since you are probably not able to report to our office behind the Creativity Shield, please hit yourself over the head with Harry Potter and the Chamber of Secrets, and speak, "The figure guarding the entrance to Albus Dumbledore’s office is called a gargoyle, not a golem".

If aforementioned book is not available, you may also use Harry Potter and the Goblet of Fire, Harry Potter and the Order of the Phoenix, Harry Potter and the Half-Blood Prince or Harry Potter and the Deathly Hallows, but those will hurt more.

Attached below are some additional notes non-Agent Hieronymus took while investigating this mission report.

The Snowdrop, Inofficial Head of Department, Uncanonical Department of Inaccuracies

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... fear tinging her voice as memories of the famous game’s implied darker side told of ran through her head.
I get that somebody told Natalie of the game’s implied darker side (and hope I got this right), but can you really say this with so few words or are there some words missing?

Natalie laughed bitterly as they walked out the room with the other wizards and witches.
I’m not entirely certain, but I believe this should be "out of the room".

Moody laid out a plan for how to to get to the test subject
Too many "to".

(In training room 4218 B:)
The agents looked at them down in shock.
I’m not aware that the agents are somewhere up from where they can look down. Should this word just not be there, or did I miss something?

... nor that the everyone else had left the room.
This "the" should certainly not be there.

Yeah, that was strange. Fortunately we weren’t forced to watch Byte replace Harry.

HG

We do what we must, because we can...
(Dang it, you have that song stuck in my head now!)
Look at me just talking when there's science to do...
(I am aware that that line is later in the song, but it's appropriate)

That's certainly one of the stranger crossovers I've seen people handle. I loved the gag at the end with Za'kiir singing "Still Alive." I wonder what happened to make Natalie that scared of the Portal games...?

Couple minor things...
"muggle-use wand"
Capitalize "Muggle".

"and laid it in the Four B Bag "
Missing a period after "Bag," and I'm not sure it should be capitalized unless it's a magical item, like a Bag of Holding. What is a Four B Bag, anyway?

"We will be adult wizard and witch this time.”"
Missing a quote mark before "we" and an "an" before "adult".

"richly-colored wizard robes clothes them both"
Should be "clothed them both".

Again, congratulations and good luck with your next mission!