I'm going to theorize because I can.

Looking back on the epilogue my eyes encountered this stained glass of the student six. I have to ask though.. what is going on here????

What is that creature they are fighting?? a dinosaur??? Are they in space?? what is happening?!

I feel compeled to create my own story from what is presented here so here we go.

One day in the magical land of equestria a giant portal opened in the middle of nowhere, and from it a group of creatures from outer space came to invade this new land full of resources, and in their scouting of this new place they found this resource called magic. 

They tried to steal it from the unicorns with their own weird powers and started conquering some places, including ponyville. But then the student six took refugee in the crystal treehouse and stumbled upon one of the invader aliens and made friends with them because it wasn't really bad but the leader is the one that is bad and is brain washing the others with it's weird justifications for war. So then they make a plan to meet this leader guy because somehow no one else can do it because they were captured or something and they are the only ones that can do it, but then this guy is like "you can't catch meeee" and goes through the portal. And then... our heroes have to go through the portal to the other planet and they have to disguise themselves to not be discovered, but then they got discovered and the bad guy is like "aha! you thought I could be defeated but you were wrong!" and in that very moment when everything looked like it was over for our heroes, Gallus stands up and says something about friendship and working with each other and everyone believes in themselves. So they all get convinced by the speech and everyone gets against the bad guy and they throw them out into a flaming planet for eternity. The student six gain an ally for equestria in this alien guys but they have to go and not conquer planets anymore so the portal closes leaving Equestria safe to live another day. And to commemorate their heroic deed they make a stained glass window that now sits on the throne room corridor. THE EDN.