Starship Magic has been destroyed, and Captain Sparkle is missing in Equestrian space. Co-Captains Celestia and Luna of the Starship Harmony must find her with help from the other five Starship Captains of the galaxy: Captain Dash with Starship Loyalty, Captain Pie with Starship Laughter, Captain Rarity with Starship Generosity, Captain Jacklyn with Starship Honesty, and Captain Flutter with Starship Kindness.
As they travel across space, they discover a new threat to their friend, and possibly the whole galaxy.