I post on /mlp/ first and here second. As such, story is in greentext format somewhat, but I write multiple sentences per line. Even still, I've made an attempt to format it for here, but understand that if the odd line/paragraph appears short, that's why.

Anonymous, as he is known in Planet Pastel Pony, is a scientist at heart. Immediately upon entering the land of Equestria, he realized that physics and fundamental laws of the universe were different, the most jarringly obvious being magic. To his dismay, the ponies had no knowledge of what magic truly was, and never attempted to find out.

Twilight, however, is aware of an unfinished project of Starswirl the Bearded, of which only rumors existed even thousands of years ago when he still lived. Anon convinces her to journey with him to the remote tower, to find this research and perhaps the answers to other mysteries.

Upon arriving, they find a massive complex beneath the humble tower, unknown to historians everywhere. It is here that Anon believes he will find the answers to his questions...

Pastebin if I forget to update here: http://pastebin.com/pUGK5fhy