What would you do if you lost your closet friends in war and you were all alone?

Years after Twilight Sparkle has been title Princess of Friendship Pegasi ponies are planning on becoming supreme rulers of Equestria. Apple Jacks normal life at home is not the only life she lives. She works at a secret agency and plans on putting a stop on the attacks. War eventually rolls in and it will soon be up to her to save Equestria. Will she be able to complete the task?