I liked how you were able to flesh out your agents' characters, especially E.V.L. She's pretty much how one would expect a Suvian agent to act! I hope to see a lot more of your work.

That said, I did catch a few things:
and even if we hate each others’ guts, I still need to know how you idiots do things around here
The apostrophe is in the wrong place. It should be should be "each other's guts".

E.V.L. decided not to pose the obvious question about how dA treated MLP:
I suggest that you cut the acronyms. Granted, it's easy to guess what you're talking about, but it might throw people off.

A second mini-Discord, Cadence, promptly poof-ed into existence next to the agents.
I don't think that the hyphen is needed.

“There never was any mention of how many alicorns the world could support at any one time,” the disguised ex-ficubus noted. “So that means this prophecy wouldn’t have been backed up by anything in the actual canon.”
It seems like E.V.L. is trying to make a good argument on the Sue's behalf; she's saying that the prophecy does not run afoul of canon.
If so, then the word that you've used is the exact opposite of the word you want: you should use "contradicted," not "backed up."

“Neat use of a title drop, but no points for you, Tara,” E.V.L. sighed.
This sounds like a good comment, but the problem is that the reader does not know the context! What is the title that the Sue is dropping?

In the following chapter, the other ponies caught up with the Sue, upon which she told them about where Twilight was...
You're using the wrong prepositional phrase. Where you put "upon which," what you really meant to say is "whereupon" or "at which point".

“Now, roll over!” Rayner ordered. Cerberus roll over onto his back.
Tense shift. It should be "rolled over".

“Then why don’t you just transfer him in External Security?” E.V.L. growled. “That way, I’ll never have to see his stupid face ever again.”
Two issues. One, it should be "transfer him to External Security".
Two; How does E.V.L. know about External Security?

Though I really have to question if 'recruit' is the proper word to describe E.V.L. :P

Anyway, excellent first (DMS) mission, and I can't wait to get started on our collab!

I can't pinpoint what exactly I liked about it, but it was good!

Good work! As someone who is still very new to the series (I've only seen a few episodes of Season 1), this was very enjoyable and a fantastic mission to read. However, the text seemed very clustered together - I read most missions on my iPad, and my brain started confusing which line I was on after a while due to the spacing. Some more space between each different lines of dialogue would be great.

Overall, though - I loved the mission!

Your agents were very interesting and with great interaction. You really get a feel for each of them. And I like that there's still plenty of animosity and room for development in future missions.

And a nitpick, "falling right after the Sue melted through the strange mirror."

(There's nothing wrong with a trope title.) Rayner's mean-spiritedness still comes across as weird to me. I know he's not supposed to be all rainbows and flowers, but... Is he going to mellow out at all in the forseeable future? (Also, remember to make Wiki profiles for him and E.V.L.)

I particularly liked the part where E.V.L. charged fake!Sombra and tried to fight him off. It really captured her overconfidence and relative inexperience with this whole PPC thing. (Also, what is the deal with her head? I thought it got reattached, why does she occasionally play with it? That's creepy even by her standards.)

Come on guys, applaud! That was great!