He opened a portal and tossed the mini through before it could cause any chaos.
That would be Counterlot, right? Two paragraphs further down:
He reached out and snagged the mini-Discord, all but flinging it through a portal.
Did Zeb dispose of Counterlot twice? If not so, who is this mini-Discord and where did it come from?

“Gwilithiel!” The scene changed abruptly to the castle and Zeb set Dawn on the ground before landing as well.
Then there is a lot of talking (and some action) and it takes seven paragraphs until
Zeb shushed the fire-lizard when a vague copy of Canterlot Castle sprung up around them.
I’m not sure whether this still can be justified by "speech is a free action".

Zeb’s shook himself and his mane suddenly crackled with sparks.
Zeb’s what? Why is there a possessive?

Despite the criticism, I really loved reading this mission.

HG

Really, real nice. It was good to see Zeb in a more relaxed situation, and Dawn's very fun to read!

You explored the repercussions of the incident without going overly melodramatic, and kudos to both of you for managing to juggle both Zeb's feelings and the mission without having either get derailed by the other.

However, there are some errors:
1) The fire-lizard had the advantage; she could fly, whereas Dawn was left dodging minis and abandoned yarn balls right and left.
Replace that semicolon with a colon.

2) I'm going to guess this is just a tragic backstory. Unless I'm proved wrong, I'm quite happy to be proved wrong.
In that second sentence, are you attempting to portray that Agent!Dawn ran through those clauses without pause? If not, then that comma should be replaced with a period. If so, then it should be replaced with an em dash.

3) How about you, Zeb, thoughts?
Similar issue as above. That comma after "Zeb" should be either a question mark or a semicolon.

4) Applebloom the mini-Discord: This one's not so much as an error as it is an observation. I don't think that "Applebloom" counts as a mini.
From the MLP Wikia:
"Apple Bloom's name is spelled as "Applebloom" in the credits of Equestria Games, My Little Pony Equestria Girls: Rainbow Rocks, Bloom & Gloom, and sometimes in IDW comics".

5) You let them hang around and bad things start happening.
Now we have a missing comma; this one needs to go after "hang around".

6) “And they’re supposed to be the human equivalent of… I think perhaps ten?”
The CMC can't be the human equivalent of anything; they're ponies. You're trying to state what their level of development is equivalent to in human years. Consider this rewording: "And they're supposed to be the equivalent of … I think perhaps ten in human years?"

7) He opened a portal to the Sue’s bedroom later that night.
Dangling modifier: as written, it can be interpreted as that Zeb waited until later that night to open a portal into the Sue's bedroom. Obviously, you're trying to say that Zeb opened a portal to that particular place and time. Please reword that sentence.

Zeb needed someone to comfort him after every thing that happened and it seems Dawn was just the right person for job. :D

By Discord, what is it with badfics and Seventh Elements? I mean, it can be done well. Pony Pov had Trixie as a second Element of Magic and the lost Seventh Element in the backstory was the Element of Trust, which actually makes sense in context of the whole friendship theme.

“Having a trajeck backstory"

Is that a typo in there or is just some term that I don't know?

It's interesting to see Zeb while he was repartnered, and seeing more of Dawn during missions is great too. Is she sugar-high or normal here? If it's the latter, can't help but imagining how the former would look like.
As for Zeb... He needs hugs, Sweet Poffins and more people saying how awesome he is. The moment where he was reunited with the Aviator must have been quite heartwarming and tearjerking.