Congrats on the first mission. I like it. {= )
First, a few things I noticed:
1. When the mini-Unas wakes Orken up, you mention him having to get his heart rate under control. I'm not that familiar with the canon, so I could be wrong, but I thought the point of the disguises was that they wouldn't have a heart rate that the Stu could detect...?
2. A couple of missing apostrophes around the "Another Excellent Chapter" author's note; one before it (authors instead of author's), one after (Suethors instead of Suethor's).
3. "Rouge NID" is meant to be "Rogue NID," yes?
4. This is for everybody: it's "all right," two words; literally, everything is correct. "Alright" happens because we think it should work the same way as "although," but the "al" there takes the medieval sense of "even," so it doesn't really. It's so widespread that in most cases no one will notice, but since we're concerned with correctness here, it's something to keep in mind.
That out of the way, in general I thought this was a good mission for establishing the baseline for the characters. I think I'm echoing the previous posters when I say I'd like to see Orken get more ruffled by Thomas, but I think it's important to show what's normal for them before you start breaking them down, so it's cool for a first mission. {= )
The Stu... I just.... Look, people, if you're going to write a character who's supposed to be really smart, you have to do the dang research, or it all falls apart as soon as you run into a reader who actually knows anything about the subject you're talking about. Argh. Was his internet signal supposed to be squiggly, or adaptive to the multiple layers of shifting atoms in the rock...? I mean, I'm pretty sure a wireless signal has to be continuous to be any good, right? You can't just break it apart and expect it to work properly. Gah.
Things I particularly liked include the conversation with Mitchell when the agents stepped in as guards, the attention given to keeping the Stu from noticing the agents, and the description of being flung from wherever they were to Cheyenne Mountain. I have trouble with Mitchell because I'm a Farscape fan first and foremost, so I have a lot of trouble seeing him as anything but an alternate universe version of John Crichton, but even with that the exchange felt in character, even with his intelligence nerfed, and it was a nice break from the Stu being dumb. I think we rely a little too much on the SEP field at times (I know I'm guilty of that), so the reminder that we should actually worry about this is well taken. And, well, silly things happening to the agents is always good. {= )
~Neshomeh