I apologize for not responding sooner - I went to see How To Train Your Dragon 2 a second time in the local theater yesterday (I would *highly* recommend visiting the HTTYD continuum in a future mission btw), and ended up doing graduate research until one in the morning! Anyway, I think everybody's covered any proofreading we may have missed (I was going to correct it myself but I see you've taken care of it), so I'll probably go into some general topics.

For Miguel's abilities, direct time travel may be a little overboard, but I do imagine that a limited version of such a skill may make traveling through badfics a little bit easier (though not very much). You won't need an RA to skip past scene shifts, for example, but you will need one both to enter/exit the badfic and to jump to a different location. It may be possible that in a badfic, Miguel could skip only one or two chapters at the very farthest, if they're not important, but in general he'd probably go past only a scene or two. At least it'll make dodging Author's Notes easier, though.

I'm actually not interested in adopting any of the mini-Missingno, sorry to say - I already have a whole bunch of mini-Omnidroids, a mini-Sentinel, a mini-T. rex, a Spellcheck Scrat, and an Attack on Titan mini I accidentally spawned myself during a post on the Board (Eren Yager, I think). Since my collab with Desdendelle also deals with Pokemon, that technically means I'll have already adopted one mini-Missingno by the time we're done with that (though it's probably gonna take a while, due to responsibilities on both sides).

One little issue, however... I was honestly surprised to see you post this thing without getting a third person to beta-read it. Granted, there were two of us working on it, but I usually get at least two beta readers for the missions I write solo (And speaking of which, I wonder why haven't PoorCynic and Iximaz beta-read my first DMS mission yet? I remember the latter being more punctual for that Teen Titans mission I did last month...). I'll let you off on this time because I didn't see too many things wrong with this mission, Board-caught typos aside, but please remember to have your missions beta-read before posting them. I'd be happy to serve as a beta-reader, in fact - you know my e-mail address so contacting me shouldn't be too much of an issue.

Regardless, great job, and best of luck with your future endeavors! :D

Firstly, and no offence meant, but are you sure that the fic takes place in the game continuum, because I've had a quick flick through and I can't see it stated anywhere for definite. The reason I'm asking this is because in the anime continuum, I believe Pokemon can learn more than four moves at once, although they can't use more than 4 different moves in any single battle.
Secondly when the Sue is scanned by the Pokedex it's said that her stats are vastly underleveled, when in fact except for her Attack and her Defense (which are actually at an acheivable level for a Level 10 Mew) the rest of her stats are overleveled, some by a small amount (Special Defence) some by a larger amount (Special Attack and HP) and Speed is ignored completely (something which isn't even picked up). Using a Stat Calculator that I know is very reliable this is a Level 10 Mews Stats with Max EVs and IVs and a neutral nature.
HP 49, Atk 34, Def 34, SpA 34, SpD 34, Spd 34 compared ot the fics stats which are HP 65, Atk 34, Def 33, SpA 54, SpD 38.

Otherwise well done.

Though it was a bit unnerving when it started rewriting itself in front of my eyes...

Anyway, yes. Fun. I thought you overdid it a bit on the infodumping between the three agents - in particular, Chris would every so often just flat out ask to be infodumped about random things, including Ami's history, which was quote jarring - but in general, it worked well. Falchion slipped between competent and newbie pretty convincingly, and the new kids felt, well, new. I also really liked the Pokemon battle at the beginning - fun stuff.

Also, mini-Missingno are adorable. ^_^

hS

Not bad for a first outing. And Arceus, did that Sue make absolutely no sense! Why would a pair of Pokémon hide out as humans? How--and WHY--would said Pokémon imprison others in an apartment complex's basement? And if you're a Pokémon, then for what reason are you going on a Trainer journey?! I'd understand a journey to figure out how to turn back into a human, but a Trainer journey? Again, why?!

*deep breaths*

Either way, good work on this mission. Not too long, and it got the job done.

There are a few errors, however:

Not having the tilde over the e in Pokémon is understandable...
Wrong word, there. The "tilde" is that little squiggly symbol that goes above the N in certain Spanish words (i.e., this symbol: ~ ).
The marking that you wanted to talk about is this one: ´
This marking is called an "acute accent". However, it would make sense to just say "accent"; unless the language being referred to has multiple accents, the word "accent" by itself usually implies the acute accent (of course, that is when the word is used of an accent marking, as opposed to a speaker's accent).

a sheep-like Pokémon with fluffy cream-colored wool and a blue head/legs.
That description is a bit awkward: it seems to say that its head is its legs. What you really want to say is that both its legs and its head are blue.
Therefore, just say so. Consider this fix: a sheep-like Pokémon with fluffy cream-colored wool, a bare, blue-skinned head, and similarly-colored legs.

I didn't warn her about the gruesome death of the Character Replacement we were supposed to kill.
Memory serving, not!Ludlow was one of multiple Character Replacements in the fic, yes? In that case, wouldn't it make more sense to change the article? That is, say "a Character Replacement," as opposed to "the Character Replacement."

He’d done it right; the Sue’s apartment complex was clearly visible through the portal. “Miguel, would you mind carrying Mareep this time?” Ami asked.
Minor nitpick here: I think a paragraph break between the two sentences would be in order. Remember that the previous paragraph focused on Falchion, and this paragraph starts of with the results of Falchion's efforts. To have the same paragraph inexplicably switch to Ami is a bit disorienting.

Falchion instinctively blocked the attack with his large wingspan before tossing the RA to Chris. It was lucky that in the Pokémon games, Normal-types are immune to Ghost-type attacks.
I was a bit confused when I first saw this sentence; it took me a while to remember that Falchion was disguised as a Fearow in this mission. You might want to make that fact a bit more explicit.

She struck out with a Stomp attack at Replacement!Mewtwo, kicking him into the wall behind him, but at the same time, a Shadow Ball caught her in the chest and sent her sprawling, somehow forced back into her human form.
That bolded word should be "forcing"; you're using it as a participle here.