The Unknown War

Description: "My sis, Applejack, says that their used to be two princess that raised the sun, and the moon. Ah can't remember it anymore, but my sis did tell me something about the Elements of Harmony. That name...has been a rumor for five years. It says it granted the power of friendship...Ah didn't believe 'em. - Applebloom.

This could use a serious re-write.
For a start, The scenes are rushed and very unclear. I can't build a picture in my head about what's happening! That's mainly due to the insane amount of questions left unanswered. such as: Why didn't Celestia notice the virus? What do the 3 different stories have in common? Who is alive? Who is otherwise? Is Equestria still a country or has it fallen to anarchy? How old is Applebloom now? Who was the opposing side in the Equestrian games? And many, many more.
Also, I don't buy Applebloom being a murderer. She's not strong enough to kill. Yes, I know she got abused every single day, but Applejack would overpower her easily.
All in all its a confusing mess.

However, It does sound like you have good ideas, and your grammar is acceptable. Not every author is capable of that.

1601523 It's actually suppose to be confusing, then more stuff is explained later in the chapters.