One hundred years ago, ponykind discovered they were not native to their planet, Equus. For the past sixty years, they have been working on a spaceship to return them to their true homeworld. The young unicorn scientist Twilight Sparkle has provided the final piece of the puzzle needed to complete the gigantic mothership intended to lead their return, a technology to fuse pony and machine into a single organism. Refusing to allow anypony else to undergo the highly experimental procedure, she sacrifices herself to become Fleet Command. In just months, the Mothership will finally launch, and an age-old journey will begin.

Elsewhere aboard the ship, six ponies who would, in another universe, have been her close friends and companions prepare. Shining Armor is commanding the vessel's final assembly, including the permanent integration of his sister into its computational core. Applejack commands life support, keeping fifty thousand ponies alive in the depths of space. Fluttershy has just come aboard as the ship's lead zoologist, a renowned expert in animal behavior whose talents will, hopefully, extend to alien life. Rainbow Dash is a scout pilot, one of the ship's complement of defenders, as well as the tip of the ship's mission of exploration. Rarity is a master machinist, ensuring that the new and experimental technology the ship is working on always has a certain artistic flair. And Pinkie Pie is a pastry chef by day and entertainer by night, ensuring in her own inimitable way the ship's continued morale.

But none of them have the power to see what awaits them in their mission...

(MLP/Homeworld crossover)