The mission reads quite a bit better than when I was betaing it. But it seems that a few errors slipped through the cracks. HG and EPL already caught the missing W in "wall," so here's the rest:

the Dedede dummy which had surreptitiously taken the canon’s place prepared to fight.
That should be "the Dedede dummy that had surreptitiously taken the canon's place"

“Wow, poor Luigi,” Honedge!Shulk said sympathetically. “Looks like that advice wasn’t enough to help him.”
“Why do you think that?”
“Oh, I don’t know. I simply made an… educated guess.”
Beat. “…It’s the ‘Green Mario’ thing, I’m guessing,” Whitney said finally.
The Shulk double nodded slowly. “Correct. Though he’s technically been a semi-clone since his debut.”
Apparently everyone else got what you're saying here, but could you please explain what you are referencing?

Once they had made sure that Not!Luigi was well and truly gone, they returned to their RC, Honedge!Shulk sat down at the foot of the single bed once again.
This is a comma splice. Either add an "and" before "Honedge!Shulk" or split the two sentences.

And I have to echo Tira here: You could have folded the "alternate" ending into the mission proper. Whay did you decide to split them?

I liked most of this, but there are two things that rubbed me the wrong way.

[...] the anthropomorphic Honedge was so engrossed in this and many other questions that he didn’t realize that he’d passed by the RC he was looking for until he’d kept walking for several minutes.
This is not how PPC HQ usually works. If you don’t pay attention, you should soon arrive where you should be, although that’s not always where you intended to go. Realizing that you’ve walked too far and trying to return should actually make it more difficult to get there, until you are distracted again. Since Flashback absentmindedly walked past the door rather than crashing into it, he apparently was not supposed to be there yet, possibly because the narrative laws of comedy required that he arrived only after Whitney got the mission, they would have no time to talk, and would go into the fic mostly unprepared. I was disappointed when this didn’t happen.

It had taken quite a bit of convincing to get Dedede to head through the portal to where Ike was, but the hammer-wielding bird had finally relented once Whitney told him that the match had been cancelled. He wouldn’t be fighting Luigi today – but there was a free-for-all open on the Gaur Plain stage, with Ike already getting ready to go.
Why didn’t we see this? It’s true that interacting too much with canons is frowned upon, but doing it off-page doesn’t help your cause, especially when you rant about "Show, Don’t Tell" in your author’s notes.

Typos:
She looked at him with frightened apprehension, but he turned to he and added [...]
The second "he" should be "her".

The humanized Sword Pokémon slammed into the opposite all, and before he could raise his Monado to defend himself, Not!Luigi had begun pummeling him, kicking and pounding.
Oh, eatpraylove already noticed the missing "w", and I don’t agree with her second point. Not!Luigi had already begun pummeling Backslash (past perfect) before Backslash could raise his weapon (past tense) looks perfectly right to me.

HG

Thanks for defending Luigi's honor. I like him better than Mario anyway. Whitney and Backslash balance each other out pretty well, but I'm confused about a few aspects of all this.

For starters, what the heck is Backslash's species? I know he's a former Stu and therefore a bit canon-breaking by default, but having him as both a Honedge gijinka and a Shulk replacement strikes me as a little overpowered. And mostly confusing. (I assume you wrote the snippet of fic he came from?) He also strikes me as a little too violent for active duty, even with the Glitter removal and therapy sessions.

I feel like you brought up the possibility of a Wii Fit Trainer Agent in a thread some time ago; if you did, props for somehow making it work. (Still waiting for Brenda and/or Vampire!Robin to get more screentime...)

My usual list of things...
-"...I thought it was the Villager who was portrayed as a psychopathic mass-murderer by the fandom, and not [– OW!]"
This doesn't feel natural. Try something like "...Usually the Villager gets the psycho mass-murderer treatment in this fandom, not [– OW!]"

Nice trick with using the dummy to protect a threatened/Stufluenced canon. (Ike was under a little Stufluence, right?)

-"...rubbing his gloved hand over his nose and noting that it was a decal on skin as smooth as glass."
Also clunky. If the point is to show Backslash's surprise at the (ingenious!) Mii Fighter disguise, try something like "'What am I now?' he asked. He ran a gloved hand over his face, then pulled it back when he realized that his skin had the texture of plate glass. Furthermore, his features felt like decals of some kind."

-"...He may need a monster to clobber that there Kirby, but he wouldn’t act that cruel by any stretch of the imagination."
Why does a character ostensibly from Smash Bros. know a meme relating to the Kirby dub?

More tomorrow, when I'm not sleepy.

Good job on the mission! I have to confess, Whitney reminds me a lot of this Rhymes With Witch strip. (Warnings for gore.)

I really like the vibe that Whitney and Backslash have going as a team. The main issue I had with the mission is that you tend to use overly long epithets for the characters. "The Sword Pokémon-slash-Homs" is a particularly notable one, as you use it multiple times. I know it's a little harder with Backslash, since he doesn't think of himself by that name, but it's a trend that occurs in all your missions, not just this one. Don't be afraid to repeat character names or use pronouns. (Confession - this is the reason I made a pair of agents of different genders, so that it'd be easier to keep track of who's who.) Also, I think you could have incorporated the "Alternate Ending" into the main fic, but that's just me being pedantic.

Overall, I really enjoyed this mission! Maybe I just have weird taste, but it's probably my favorite of your missions.

This was really good!