The story is great.
I found a few typos.

Aside from the annoying comment, he’s got me pegged. “The not running part had crossed my mind.” I looked away, not happy that he was just waiting for me to ask. I hate being toyed with, and I won’t give him the satisfaction of me asking. “You’re flanks? Not so much.”
Darn it. Your instead of You're.

“Stim Pack, get over her NOW.” I shouted, not even noticing that the old, grey bearded pony had been face down on his desk when I entered. He didn’t budge as I waited for a response, instead letting out a soft snoring. I picked out one of the mostly empty bottles of alcohol on his desk and bit down on the neck, swinging it down hard and shattering it.
First, you lost an 'e'. You mean here.
Second, snoring is an action, snore is the sound you make while snoring.

I could hear him grumble as he gathered up his tools from amongst the clutter of the other room, finally joining us in the back after a minute. Both Short Staff and the Pegasus had been placed on the two surgical tables in the room, and we stood idly by as Doc Stim Pack came in and gave them a quick look over. He turned back to us with a sigh.
There's no reason to capitalize Pegasus in the sentence.

3755788 *nods* I'm aware there are a few typos here and there my editor is taking a look at the chapters and updated versions should be out soon. I'm glad you like the story!

Well at least she didn't die, good chapter

“I believe the score is Predious one, Storm zero.” He looked to me with a smirk. This might sound wrong but I hate unicorns and their cheater magic. I tried standing up to aim again, but only found myself dropping back into cover just as I pulled my sights up. If only I could get a few more seconds…
My display changed to pink as Pai popped up. “It looks like you are trying to fight more efficiently. Would you like some assistance?”

Lawl.
That is, I laughed. Well, more like chuckled, but I was amused either way.