Interesting interaction between your characters, and even if the badfic was boring as all get-out, at least the mission was a page-turner, metaphorically speaking. I wonder what the future holds for Cupid and Stephanie.
Well, you literally asked for it, so here's what I caught:
1) She closed her eyes and concentrated; in a flash of color, she suddenly looked like a deluxe-sized, female Cupid.
You make it seem as if she transformed into an angel instead of changing color. Try something like this:
She closed her eyes and concentrated; in a flash of color, she suddenly looked like a deluxe-sized, female Cupid, albeit wingless and with tentacles for legs.
2) There you are, you had me so worried!
Technically ungrammatical (replace the comma with a semicolon), but it might work if you actually intended for Lapis to say her lines that quickly.
3) I am in fact the first boss of the game, the Mantis Ant.
Is Chakkik supposed to be the selfsame character, or is he just the same species as the boss?
4) Disguise-Outfitting Ryticular Costume System.
Ironically, you're misspelling something by using the correct spelling. "Costume" here is to be spelled with a "K", not a "C", hence the acronym D.O.R.K.S.
5) blue dorsal/anal fins
Replace the comma with the word "and."
6) [Cupid] had large, flowing fins where his wings would be as an angel. Or, in this case, an angelfish.
I suggest that you delete the last sentence. I don't think that angefish have such fins. Besides, you already mentioned his dorsal (back) fin a few sentences earlier, so these fins would be in addition to that one.
7) Taking out the (thankfully waterproof) RA, Cupid put a hand to his ear, delighted to realize that the sound of the Words travelled much further while underwater.
Huh? Unless I'm mistaken, agents can only see the Words, and that by unfocusing their eyes. I'd suggest deleting this sentence and replacing it with something else indicating that he was checking the Words.
8) I am no scion of Sylph.
Misspelling. The name of that particular spirit in Secret of Mana is "Sylphid", not "Sylph".
9) “Wait, him? So, you like guys or something?”
Just a style suggestion, but put "him" in quotes or italicize it.
10) The last time I brought the subject to my orientation, my companion at the time had a panic attack.
Should be "The last time I brought up the subject of my orientation".
11) Stephanie might have been an eleven-foot kraken, but she remained an octopus,
That should be "part octopus"
12) The agents poked their heads out of the water, staring in morbid fascination at the sight of an unidentified pirate captain declaring that Undertow was “you’re new master” before giving him some kind of amulet.
As much as I like picking on badfics' lack of grammar, you're actually amiss. Here's the context:
"Are you the Undertow?" the captain asked.
"Yeah," replied Undertow. "Who's asking?"
He then sees the captain smiling as the human uses his sword and moves it close to the shark's throat. "You're new master.
Your/you're error aside, it's clear that the pirate captain was calling himself Undertow's new master. A quick fix is in order: "The agents poked their heads out of the water, staring in morbid fascination at the sight of an unidentified pirate captain declaring to Undertow that he was “you’re new master” before giving him some kind of amulet."
13) The kraken looked puzzled. “Why, what does Cupid have to do?”
Try this instead: "Why? And what does Cupid have to do?"
14) "James" came right out of nowhere; I do not recall him being in the badfic. Where did he come from?
15) I know that Lapis said that she'd only keep one pov, but she sent two to HQ via the same portal. Where's the Normal pov?
16) We can buy them from the Armory with our own pay!
Pay? What pay?