The CMC find a ruined city at the end of a deep cave in the Everfree.

Twilight figures out it's actually a factory.

A factory for building starships.

With a vessel in hoof and a jump into Hyperspace later the mane six are off to meet their neighbors from this region of space, from the nice, the crazy, to the reasonably evil.

This is a crossover with Star Control 2, which you can download and play free here.

If you haven't played the game yet stop reading and go play it, I promise it will only take a few hours... If you write down every piece of dialogue you hear.