I think you did a good job in this mission of laying out the tension between Lilac and the more veteran agents. The question of Lilac’s identity is constantly on all their minds, but rather than having the characters talk about it bluntly, you let it simmer in the background. It bubbles out into the dialogue occasionally, but mostly, you communicate it through speech tone and facial expression. That said, I’m not totally on-board with the conclusion to the conflict. Right in the opening scene, you establish that while Lilac believes herself to be a Violet Parr, she already recognizes that doesn’t necessarily make her the same as the one in the movie:

"'I know it sounds weird, coming from someone who diverged from Vi a long time ago, but I at least have the decency to take her character seriously,' said the newbie."

[Sarah] still couldn’t believe that the new girl had yet to accept that she was not, in fact, an alternate-universe Violet in all but name.

This at least shows that, even if Lilac is choosing to believe herself the canon Violet, she also recognizes that alternate universe versions of a character can exist, and she even refers to Violet as a separate character. So at the end of the story, I don’t understand Lilac’s surprise when the Violet in the fic turns out to be the real one. It seems to me she was already aware of the possibility of other Violets being real, so potentially, this wouldn’t even change her beliefs. Is there some aspect to her character or history I’m not understanding?

I liked that you had your agents discuss the fact that Team Fortress isn’t a very rigid canon, and that they weren’t judging the badfic on that angle. I like to communicate in the mission when things aren’t charge-worthy, or are only ambiguously so, so it’s good to see other PPCers do the same! I also loved the gag behind the disguises. Very clever!

Some typos:

"'Team Fortress 2,' Sarah explained. 'It’s like, this darkly comedic team-based first-person shooter. That’s where the Spy is from, and I think he’s a lot older than, say, Tony Rydinger, for example…'
'I’m not so concerned about that.' Sarah punched her palm. 'Isn’t Vi only fourteen?!'"
Sarah is talking to herself.

"'Besides, I’ve been wondering…'
'Of what, exactly?' asked Falchion, earning him a slightly annoyed look from his adopted sister."
I’m not familiar with "wonder of" being used as a verb phrase. I think you can drop the "of" here and retain the same meaning. It sounds a bit awkward to me this way.

"The agents stepped out of the portal and back into the base, abandoning a plate of cold bacon that had been sitting there in the kitchen. Said bacon was gone in a matter of minutes, courtesy of Falchion."
For me, abandoning food means not eating it. Unless you meant they’re abandoning an empty plate that formerly contained bacon? But "a plate of cold bacon" reads to me as a plate still containing bacon, so I’m a little confused about the meaning here.

"The agents hid in the very darkest corner of the room as her gaze fell upon them the men before her, and then focused on Violet herself."
Extra word.

"There was this one time, for example, when she and the canon Stratogale had laid eyes, and the poor agent had gone into a minor existential meltdown, not that she’d let her companions know it."
I know this phrase as "laid eyes on each other." I’ve never seen "laid eyes" used in that shortened form before. If that’s longer than you wanted in that sentence, you could also potentially use "met eyes."

"'Maybe it’s ‘cuz she’s too young for the job?' asked Sarah.
The agents were silent for a few moments.
'Or maybe,' she mumbled, 'that is NOT the real me.'"
I’m pretty sure that "she" is supposed to be Lilac, but as these sentences stand, it sounds like it’s Sarah speaking more.

"'. . . by order of the Protectors of the Plot Continuum, you are hereby charged with being a character replacement on account of willingly agreeing to being conscripted to the BLU team, knowing full-well that they can’t care less about the lives of others, and are willing to take them if it means getting paid.'"
That "them" is out of place in this sentence; there wasn’t really a plural noun before it for "them" to serve as a pronoun for. Were you maybe wanting to say "take those terms" or some-such?

—doctorlit in a busy week

Aka I didn't catch any odd SPaG mistakes, everyone's voices were distinct, and I felt that Lilac's dramatic arc was executed with proper taste. ^^

The best bits were the recurring arrows - or rather, the scene dividers and then the decisive arrow! - and the hugging-the-shield scene at the end.

Here's to the new year, and new missions!

I'm still wondering just what on earth Ri2 is doing, mind, but that's neither here nor there.