but that appears to be my main occupation hear.

“A seven exclamation mark mission, it must be bad.” He said, glancing over his shoulder at his partner before turning his attention back to the screen in front of him.
And
“My name is Agent Steven Fontwell of the Protectors of the Plot Continuum.” He told her, pausing for dramatic effect.
Dialog followed by a speech tag, like "he said", should end with a comma rather than a period; the speech tag shouldn’t start a new sentence.

There are more tense shifts than Pippa’s Ghost noticed. If you don’t bold these parts of the sentences, because they aren’t direct quotes, but you still use present tense intentionally to mimic the badfic, some lamp-shading is required:
Steven paused as Carl begins to ask Riley ‘The Questions’, waiting to hear how she responds.
And
“Choo wa.” Wallis responded, pulling the RA from one of his many pockets and quickly activating it, teleporting the two of them within sight of the prison as Carl and Riley make their way towards the gates.
And
The two agents heft up Riley’s body, throwing it through the portal and into the middle of the Zombie herd in the cities center. ("heft" should be "hefted", and doctorlit already noted that "cities" should be ""city’s")

“You, are Riley Anne-Dixon, a clear Mary-Sue, and are charged with the following:
Either the first comma should not be there, or "are" is misplaced. This should read:
"You are Riley Anne-Dixon, a clear Mary-Sue ..."
Or (better?)
"You, Riley Anne-Dixon, are a clear Mary-Sue ..."

The knife slashing against her throat Riley collapsed, first to her knees and then face first onto the floor glitter and blood spraying the walls of the cell and the two agents.
Pippa’s Ghost already noted that there should be a comma before "Riley". I think there should also be a comma between "floor" and "glitter".

I should volunteer for beta reading more often, even when I don’t know the canon and barely remember the agents. My laziness promptly came back to bite me here.

HG

I'm so happy you're publishing again! You have such a nice, straightforward writing style. And you get the characters' personalities across with so few words, even in such a short fic. Well done!

To add one typo to Pippa's list:
" . . . into the middle of the Zombie herd in the cities center."

So, Steven and Sasha are parents now? I only recently read their training stories, so it's a shock to see how much time has passed for them.

The mission was good. I could follow it all, despite not knowing the continuum.

You did make a couple of little mistakes:

Almost as soon as they get there they can hear Daryl Dixon shouting at the pair of them.

This needs to be in either bold or past tense, depending on whether or not it's quoted from the fic.

Steven shoot back at her, a grin on his face as he pulled a knife from his belt.

Should be "shot back".

Realization beginning to dawn on her Riley turned to try and grab her knives
and: The knife slashing against her throat Riley collapsed

There should be a comma before "Riley" in both cases, unless she really does have her own Riley and her own throat Riley.

Sorry for nitpicking.