1) “Wait, who’s turn was it last time?” said Sarah.
"Whose", not "who's".

2) The terrified ex-Sue plot-holed away, and [MUTO] smashed into another building and killed 23 more people.
Generally, numbers should be spelled out. However, I'd like to have someone else weigh in on this as well, since it's clear that you're mocking an earlier line from the badfic.

3) Seizing his long snout with one clawed forepaw, he proceeded to rip into the struggling replacement’s furry chest with the other to get him to stop moving. Then, grabbing his mouth, he forced it open, the glow already starting to spread to the plates on his back.
This paragraph confused me. In context, I can tell what you're going for, but the paragraph itself has a few issues:

a) Seizing his long snout with one clawed forepaw, he proceeded to rip into the struggling replacement’s furry chest with the other to get him to stop moving.
It's clear from context that the mini-Godzilla is supposed to be the actor here. However, I doubt that Sonic's snout can plausibly be described as long. Couple that with the massive amount of pronouns, and this sentence can be a pain to muddle through. I'd suggest deleting "long" and replacing the "he" with the mini's name.

b) Then, grabbing his mouth, he forced it open, the glow already starting to spread to the plates on his back.
Common sense would dictate that the mini would have to let go of MUTO!Sonic's chest so that he could use both hands to force the replacement's mouth open. However, the sentence structure implies that the mini is holding on to MUTO!Sonic's chest and forcing the replacement's mouth open at the same time--a physical impossibility. Consider this fix:

The mini-Godzilla then grabbed the replacement's mouth and forced it open, the glow already starting to spread to the plates on the mini's back.

4) Speaking of minis, one more question: How is "Cloverfield" a mini? Not knowing the canon, it looks correctly spelled to me.

Your agents are very brave. I have no idea who these monsters are (besides Godzilla), but I liked what you did there.

May usual nitpicks:

Around ten minutes minutes later...
Too many "minutes".

...wishing he’d bought his Angel Bow.
I suspect you meant "brought".

...his jagged spikes began to break the surface even before he even began lifting his great bulk out of the sea.
Aren’t these "even"s a bit repetitive?

...he curled up into a ball and attempted to roll over the Lapis.
Should this "the" really be there?

HG

Look at me, writing (what I think is) ConCrit. I do apologise if the tone's a bit harsh, I've some problems with not saying things bluntly.
First things first, the exposition about Godzilla's moral is a bit ham-handed, it could be toned down with no loss of interaction or characterisation.
Second, I'm uncomfortable with Sarah and Lapis mentioning their author. Most PPC Agents don't know they're characters. There's a reason Swan's Egg is a big deal, after all.
Third, capitalisation minis are frowned upon, as far as I'm aware.
Fourth, I think that missions don't need soundtracks. Those notes just throw you out of the story, and anyway a good story stands on its one even without attaching music to it. A story isn't isn't a movie.
Fifth, Lapis' rant near the start of act two could use with some toning down – that's Excessive Emphasis right there.
Sixth – I mislike Cupid's sudden Genre Savvy. Isn't he a ditz? That simply doesn't fit.
Seventh – urm, I think if a Stu throws an agent OOC, they'd be under the Aura of Smooth and generally dizzy, not up-and-about...?
Eighth – I hope Lapis using her Sue powers will have consequences later on. Agents aren't supposed to rely on Sue powers.
Ninth – I'm pretty sure it's meant to be “Excuse me” and not “Excuse you” (near the start of the post-mission part).