I have some little nitpicks...
First, Voyd, the Nyan Cat Song, is actually a sped up version of "Nyanyanya!" by Hatsune Miku, so it actually doesn't say "Meowmeow..."

And Skarm... I have some issues with the way Lapis speaks. Is she using fangirl japanese, or is she supposed to be a native Japanese speaker trying to speak English? Because, if it's the first one, that rubs me the wrong way, and if it's the second, is done wrongly and feels offensive. Take your pick.

And... which continuum was the host continuum? The Little Mermaid or Pirates?
Because if it was the former, guys... I have bad news for you. Guys, you pretty much kidnapped Davy Jones, his crew and the kraken from their native continuum and plopped them into another without returning them home.

If it was the latter... well, I have bad news too. Guys, you also got a Geographical Aberration, as two non-canonical locations would have been plopped into the world of Pirates of the Caribbean, and you forgot to send back all the canons from The Little Mermaid, back to their Woooooorld~ (heheheh)

Aside from that, I found the Mission enjoyable and entertaining.

Also Voyd, there's something that Skarm and me have to speak with you, but that should better be left for G-Hangouts.

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?

Your agents and their interactions are hilarious.

Unfortunately, there is apparently a continuity error:
“Oh, yeah, I forgot about you guys!” she said, opening a portal and sending the povs to HQ.

Lapis began breathing fast, hugging both her pov and her monkey so tightly that it was hard for them to breathe.
Either the sending to HQ should not have happened, or this pov should not be there. (Was "Melody’s pov" dragged back when the badfic changed point of view again? We should have seen Lapis’s reaction to this event. The "Normal pov" may have respawned with "The Artic" on page 22, but then it should be with Stephanie and Cupid. Also, I wonder what the Artic looks like and why it causes coldness.)

The agents (and their companions) fell silent, watching the fic play out.
As far as we know, Triton the Oshawott should be Lapis and Chakkik’s only companion at this time.

Then she opened a portal before leading Chakkik, Triton, and the povs to the same little beach as before.
As far as we know, the povs should not be there.

Also, there is a weird sentence:
Chakkik silently killed more of the Generic Pirates, avoiding Deadnite and Titus until it was absolutely necessary.
I see what you mean there, but isn’t that what was absolutely necessary in the end the opposite of "avoiding Deadnite and Titus"?

... Chris could only watch helplessly as the tentacle that had captured him from lifted him a hundred feet above the sinking ship ...
Either one word too much or some words missing?

And as Christopher Sparrow screamed his last, Davy Jones’ Kraken dragged the remains of Captain Deadnite’s ship, and every single one of its remaining crew members, down into the depths of the deep, dark, Scandinavian sea.
Missing word? I’m not entirely sure whether, in English, it is necessary to specify whether this was his last word or his last scream or whatever. (In German, the sentence would work as it stands, if "last" were capitalized to show that it is used like a noun and meant to be the sentences object rather than an adjective to this object.)

On that note, I would to extend a hand –
Missing word?

HG