Well, the Prophecy thing is kinda cliche, but other than that good start! Nice foreshadowing by the way.

Dang, that's dark!

The switch between point of views fourth wall anyone?

6853515 You'll find out why later. There is a reason.

6854018 Ok and according to my calculations you should have another chapter out in three to four days.

6854047 The third, maybe, but I have school, and with most stories, I work on the first few chapters back to back. After that, at least once a month.

6854050 Wow dude i hope your holding up with you writing stories for your followers and writing documents and other school realted things that needs to be written.

6854070 If I wasn't. do you think I would make this story?

6854071 Touche
But how long is the next chapter gonna be?

6854077 No idea.

6854086 Ok
I know this a weird question from a guy you just wrote too but would you like to become my friend? Its just because i dont have that many friends on this site and i thought you would make a perfect friend.

6854090 Not at all.

6854109 Thank you Loneshadow

6854112 No problem.

6854050 You didn't message me... Did I miss something? Or are you going without a prereader past the first chapter?

6854132 Sorry. Once third's is done, I'll send you a link.

The entire story is.... I don't know..... Not bad per se, but maybe .....weird a bit? Yeah let's go with that opinion.

But more importantly! Quips for stuff I think might be changed.
I'm not sure Josh's description is necessary to be so accurate or he just went off a tangent.
The plural for pegasus is pegasi.
Change that "Twilight-1st", to POV, or point of view, it seems a bit off currently.
Also, somehow separate the storyteller's comments (maybe italic and new line?), this way it's a bit confusing.
I find the prophecy a bit too to the point. I mean we need prophecies more vague and cryptic! Maybe instead of the "black and red being with no qualm of killing" You should say "A dark demon bathed in blood" or something like that. That should be cryptic enough for ponies to freak out and come up with any number of theories. Also you can say it refers to Josh, since his ACU has red and doesn't worry about killing.

I'm too lazy to look up all of the typos, but you have a few.

Let's do this. Second run. Brace yourselves it's long.

I pressed the middle finger button

The way you wrote it it's like the button is a middle finger :D. Try: "Pressed the button at/with/under my middle finger".

I say to

Switched to present tense.

I cued up

queued

anything to use to use strategic zoom

I'm not sure how startegic zoom works in the game, but even if it's linked to certain units you should say "to be able to use" or somesuch.

four factories of land and air at each

Four factories of [...] each. At is unnecessary

turned the factories to where the open end...

That entire sentence is a bit of a "what?" I literally don't understand which direction are you pointing the factories.

complicated cue

queue

One, I had finish my energy array

Again a bit of a "what". You had engineer one finish the array?

groups of five spaced well apart, with would

comma after "five" and "which"

Four would handle the most important right now

Either "handle what is the most important..." or "handle the most important thing..."

two air factories, which I would give

for which I would....

nuke Canterlot to hell

I like this guy.

set to building AA clusters

I think it is "set to build"

shot gun

Shotgun, one word. (though for air targets a shotgun is rather useful, but not important here)

pegasai guards

pegasi (From what I found actually "pegasuses" is correct as well. Huh.)

In the Aeon case,

This part is entirely unnecessary, as you just started talking about them in the previous sentence. And "Aeon's (i think), or Aeon units'. (Chrome should be a bloody awful camouflage, even with different colors. Armies use matte for a reason. But meh, videogames)

every thing

Everything

I put the land factories to teching up

"Set", "ordered", or similar. "Put" doesn't really makes sense here.

anti air flak

Anti-air. Also Flak means anti-air (the German word for it, shortened), so one of them is unecessary.

days later from when I began to build the base

He just planned this whole thing to this extent and this was not the building part? Holy cow.

as that has

I think you should go with "as she has"?

Of what he said

"From what he had said" (I am on really bad terms with this tense, so it might be wrong)

Still didn't excuse him

"Still, it didn't excuse him." If you are referring his killing Tirek being a baaaaad thing.

Of cours,e he did do that later

Comma at wrong place. Also, he did What later?

it was on conspiracy to do so.

Umm conspiracy? Should I grab my tinfoil hat?

What's that, auntie,

What's that auntie?

I believe it clear what you all saw

"I believe it's clear that what you all saw " or "it to be clear"

Oookay, so I feel like coming up with a better prophecy, mind if I PM you the results? No offense, but even if it's just Celestia talking about the gist of it, it's rather flat.
Some of your senteces could also be broken apart to some smaller ones.
Also when I'm not studying, I can do some prereadin' (haven't done one in my entire life, but you need to start somewhere).

"Yep," Applejack said. "Ah mean, it had horns and was colored red with a hint of black."

It's a red and Black OC, KILL IT.

All your base are belong to us.

Aww, but I like tech-wank... I'm an avid Spacebattler after all :)