At Discord's urging, Princess Twilight hops on through the mirror portal to Canterlot High, which had been closed for two millenia. Instead of a school, she finds herself in a cargo bay of a starship. Discord also has popcorn at the ready.
The ES Harmony, the pride of Princess Twilight Sparkle and Equestria's first FTL capable starship. It is due to make its maiden voyage to travel further than anypony before it, and yet its first mission... may be its last.
A distant civilization of ponies, removed from Equus millennia ago, send an expedition to their ancestral home to solve the mystery of its strange orbit. They bring a foreign mindset and powerful, conflicting interests to the peaceful world.
As a joke during his original rule, Discord sent a group of ponies to a distant, inhospitable planet and left them alone. Thousands of years later, their descendants notice a star in their sky orbiting inexplicably around its planet.