This mission was some tricky subject matter, but I think you handled it well. You kept direct quotes from the fic down to a bare minimum, which gave me just enough information to know what was going on without forcing clear mental images on me. It's also a good choice in this case to have the agents check ahead and prevent some of the worst stuff from occurring at all—not just the scatological stuff, but also the nuclear explosion. Cleaning up a canon city from that kind of destruction could be an interesting interlude on its own, but would be a bit too much to tag onto the end of a short mission.
It's been a long time since I read any of Sean's previous appearances (I had forgotten he had blue hair and piercings), but I at least feel like you've done his character justice. It would have been a mistake to make him overconfident and domineering just because he's an Original Series character; I think keeping him meek and submissive, even towards the newbies, was the right way to go. Especially considering he's apparently been wandering Middle-earth for decades up until this mission. I do love that even after being gone for decades, the Queen Anne's Lace immediately sends him on a training mission right after he got back!
I like the pair of agents you've introduced, with a rash but active one and a more reserved but overly analytical one. I think they'll make for a good team going forward. I would like a little consistency on Hurley's name, though. In this short story, she's referred to alternatively as "Melissa" and "Hurley" throughout, and then says near the end to call her "Lissa." I would think she's more likely to bring up her preferred nickname when she first introduces herself to her partner or Sean. Keeping each character's name consistent helps the reader keep track of dialogue tags and action when a lot of characters are on-page at once.
I like that you included the moment where Hurley shows sympathy for Sam. I agree with her lack of fondness for the live-action Transformers films, but I also agree that this fic went way too far in its treatment of Sam, and I like that the narration there serves as both an in- and out-of universe acknowledgement of that.
I do want to point out that you sometimes split a single character's action and dialogue into multiple paragraphs. It makes for easier reading when those things are kept together. For example, in the exchange:
“This… that’s… oy,” she spluttered. “They’re giving us that for our first mission?!”
Melissa snarled.
“I’m going to kill someone,” she spat, and was out the door before May could react.
The first paragraph has May speaking. A new paragraph starts, which my brain expects to be about Hurley, and that proves correct. Then another paragraphs starts, which my brain expects to switch back to May, but instead, it continues Hurley-based action, with May only getting mentioned at the end. It would read better as:
“This… that’s… oy,” she spluttered. “They’re giving us that for our first mission?!”
Melissa snarled. “I’m going to kill someone,” she spat, and was out the door before May could react.
Keep an eye out as you write for places like that.
Also, one little typo:
"Scene change, God and the author only knows, and hey, Jean Grey’s arrived!"
That middle fragment has a plural subject ("God and the author"), so the following verb should be "know" instead of "knows."
—doctorlit, eating second breakfast