After a natural cataclysm destroyed their homeworld and the Equestrian nation scattered to the stars in the evacuation, the Main Six and their immediate family in Ponyville drifted among the stars in an escape pod for weeks before they were found and adopted into the crew of the Federation Starship Voyager.

Just a normal day traveling through the 'verse on Serenity, then Mal finds that his ship has been invaded by talking technicolor ponies, and the crew didn't tell him until 10 minutes after.

A RWBY alternative universe crossover anthology series inspired by the Marvel Cinematic Universe, the fanfictions Viridescent by darkfire1220, and Team STIK (Strike) by Aragon365.

Celestia is the greatest huntress in all of Remnant, inspiring a generation of young children to grow up and become huntsmen and huntresses themselves. Sunset Shimmer, among the inspired children, is a timid and quirkless girl who discovers Celestia's debilitating injury and secret behind her power, and becomes entrusted to inherit the secret power of "One for All".

Secrets appear to be commonplace at Beacon Academy as secret after secret comes to surface, making high school much more interesting for Sunset Shimmer, her team, and just about every other student in Beacon.

Greater list of this being a crossover with (in no particular order and to varying degrees) (partially incomplete due to my paranoia with spoilers and to curb unnecessary expectations):
Fairy Tail, Metroid, Marvel Comics, Legend of Zelda, My Hero Academia / Boku No Hero Academia, Star vs. The Forces of Evil, Octopath Traveler, and Fire Emblem.

MLP short fanfiction based on the Phineas and Ferb song of the same name. Set in the Nightmare Moon timeline.

An alternate universe where Twilight and the rest of the main six have younger, nearly identical, twin brothers. All of whom are preparing for the Summer Sun celebration before Nightmare Moon oh-so-rudely interrupts.

Warning: Alcoholic references

Twilight Sparkle has turned evil and is bent on taking over Equestria for herself; she has already killed Applejack, Rarity, Rainbow Dash and Princess Celestia, stealing the Elements of Harmony, using their raw power to destroy anyone who stands against her path to total domination. Pinkie Pie and Flutterhsy evading Twilight's pursuit, with their respective Elements of Harmony in hand, Twilight enlisted Discord to draw out the two remaining elements by turning all of Equestria into a post-apocalyptic wasteland, and when that didn't work she released all foes she had previously defeated, including the likes of Queen Chrysalis, The Dazzlings, and Lord Tirek.

Sunset Shimmer, a former student of Celestia's, now works as a smuggler for anyone with good enough cash, all while avoiding rival employers and Twilight's Royal Guards, dubbed "The Alliance" by her and other smugglers.

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Inspired by works such as: Star Wars, Firefly, and Fallout
Art by bakki

Edit (2/10/18): Revised almost everything, up to chapter 7 and the title.
Edit (5/31/21 - now): edited for better, more consistent terminology, word choice and other cringey things.