Okay so this is my first critique so this will probably be bad. Here goes.
I'm not going to comment on grammar and punctuation since that isn't my strongpoint.
To be honest, it's a little weak. My guess is that you were trying to instil fear into the reader but it didn't do anything for me. It was pretty boring and bland to put it simply. I know this is only your first draft so I'll try not to be too harsh.
I'm noticing a lot of the word 'he', which gets really repetitive. Readers don't like to read the same word over and over, now I'm not saying to stop using 'he' but just lessen its usage. An example being: "He thought about it. A haunting realisation came over him; they'd already had a drill that month. This was real."
Could be changed into "Thinking about it, a haunting realisation came over him; they'd already had a drill that month. This was real."
The story could also use a few more details, as someone else said, we could use more details with the medals. What does Stephen look like? How old is he?
I'm confused with this part:
"This, though, was not a drill. He had never gotten used to the booming noise. He had once joked that it was enough to wake a person from a coma, a stern look from his superior silencing him. For the first few seconds, he didn't feel the burning sensation on his leg. He leapt into action as his senses returned to him. His hand wiped the boiling hot noodle soup off of his trouser leg and as he pushed himself up to his feet. Stay calm, he told himself, it must be another drill. He thought about it. A haunting realisation came over him; they'd already had a drill that month. This was real."
He says it's not a drill, then realises that's it's not a drill?
I think some of the vocabulary could be changed a little here, words like 'blaring' 'rushed' 'red flashing lights blinking on and off' are examples of things that need changing.
All in all, I found it a tad boring and cliché but I reckon if you fixed some things up, it would be a pretty good story.
Hope this helps :) (also I'm on mobile so sorry about the formatting)