Note: This starts before season 2 and slowly works its way into season 2 and then 3, so please, let me know if I've made any mistakes. I prefer constructive criticism over destructive though. Another thing, it does not begin in Equestria right away. It will lead up to it later on. I'm also giving this story a song
hero by Skillet

The universe works in mysterious ways, and for every universe, there is a sentient race, unaware of the other's existence. In the world of Equus, the land of Equestria, there exists a sentient race of multicolored ponies, ranging from earth, pegasi, and even unicorns. Little do they know, however, that there is a mysterious masked figure watching over them from a distance, waiting for the right time to show himself. For his destiny is not to protect mankind on earth. No, the god of that world has that taken care of that. Instead, his destiny, his fate, is to stop a rising evil from changing the world of Equus into a cesspool of death and destruction. And, perhaps, along the way, something will happen to him that he cannot even begin to understand.