The Multiverse is a collection of infinite timelines that, presumably, spreads across the entire My Little Pony franchise. It is the 'setting' in which every My Little Pony story ever told takes place within.
Concept history and evolution
A handful of early stories involved the travel between different 'worlds', for lack of a better definition. My Little Pony: Rescue at Midnight Castle and similar plots featured the "human" world and "pony" world of Earth and Ponyland, though the connection or differences of these two worlds were often vague. Another 'world' depicted in the original series was the Land of Legends, a location where figures of myth and literature such as Robin Hood and Hercules called home, which was located beyond a golden door.
In 1985, the long running My Little Pony Comic began its publication, which followed a much different continuity than the cartoon, instead taking place on a completely fantastical world rather than the...confusing world the animated series took place on. Generally speaking, this continuity was more similar to the picture books released around the time.
In 2013, My Little Pony: Equestria Girls introduced the concept of the multiverse formally into the franchise, which once again featured a 'human' world, but this time explicitly stated to be another universe. The following year, Reflections would flesh out this concept by telling a universe hopping story that focused on the mysterious dark universe. The concept of the My Little Pony multiverse would appear several more times in the comics by IDW Publishing and Seven Seas Entertainment, being a major element in the storylines of, My Little Pony: Legends of Magic, My Little Pony: Nightmare Knights, My Little Pony/Transformers, My Little Pony: Generations and My Little Pony: The Manga.
The concept of the multiverse in the animation of My Little Pony has been rarer, but not unheard of. Aside from the existence of the Equestria Girls universe, "The Cutie Re-Mark" featured several splintered-off timelines thanks to Starlight Glimmer's time travel shenanigans and Equestria Girls: Sunset Shimmer's Backstage Pass had a similar premise with Sunset stuck in a time-loop, altering it bit-by-bit, though it was never confirmed if these were alternate universes.
At some point, there was a "crisis" of infinite Equestria's.
The Pony of Shadows attempted to destroy the multiverse by tapping into the infinite power of Princess Celestia and Princess Luna but was thwarted by the Pillars of Equestria, though he never stopped trying. It was implied that he took down a number of worlds before his defeat, however.
The My Little Pony multiverse is, in some way, connected to the Transformers/Hasbro multiverse, as confirmed thanks to the existence of Primax 613.28 Lambda and Tyran. According to Vector Prime, however, My Little Pony is mostly fictional in his multiverse.
Early drafts of My Little Pony: The Movie was going to be set in the Hectorverse, better known as Primax 984.17 Alpha or OG001 Spacetime, the shared universe of Transformers, G.I. Joe, InHumanoids and other Sunbow Pictures properties. 
- Alternative histories
The Earths were a series of universes Discord traveled to. They were named Earth-1, Earth-2, Earth-3, Earth-52, Earth-616, Earth-Fawcett, and Earth-Z respectviely. Their name were parodies of the universes seen in DC and Marvel comics, with Earth-1 and Earth-2 being the primary realities in DC's "pre-Crisis" continuity, Earth-52 being a reference to DC's use of the number 52, Earth-Z probably being in reference to 'Marvel Zombies', Earth-Fawcett being a reference to Fawcett Comics, and Earth-616 being a reference to Marvel's main universe.
- With My Little Pony Tales beginning the trend of rebooting the franchises every decade or so, this can be considered the 'true start' of the multiverse in My Little Pony fiction.
- A number of stories in the My Little Pony franchise have been either aggressively retconned or never fit in continuity to begin with and thus can be considered alternate universe in their own right. Several of originate in IDW Publishing comics, which have...a complicated history with canon, to say the least. The most drastic of these was their incarnation of King Sombra, who has a radically different backstory, arc conclusion, personality, and even species in comparison to his cartoon counterpart. He had a redemption arc in the comics!
- Reflections - Part II: "Back to Where You've Never Been Before"
"Could there be more alternate universe out there? Who are we in each one of them? There's an infinite number of possible selves! And of those selves, who is the real you? It's fascinating. Truly a lifetime of research is to be had in the simple idea of traversing the interdimensional cosmos! EEE!"-Twilight Sparkle
- My Little Pony Annual 2013 - "Sunset Shimmer"
Crisis of Infinite Equestrias
- Legends of Magic #1
"Princess, our world is only one of many. There are an infinite number of worlds all around us."-Starswirl the Bearded
- Nightmare Knights #1
- https://web.archive.org/web/20220417003055/http://joeguide.com/interviews/buzzdixon.shtml Interview with Buzz Dixon]
- Friendship is Magic #77
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