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Well, we are a few days before the premiere of My Little Pony G5, and we know that the movie is already being leaked on the internet, hopefully there are not many spoilers … so I have come to wonder, what happened to Equestria?
 
After checking out some MLP comics and watching the What if …? by Marvel.
 
I came up with these theories, obviously these would not be 100% correct (or make sense), but I will leave you some ideas to make you think.
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Background Pony #6EF3
I really wish the story was a bit different so that it would give more of a firm reason why the ponies were separated in the past.
Background Pony #EB46
Theory 1 is pretty ingenious. If they don’t go with that, I can see plenty of fanfic material for it in future…
Background Pony #FB1D
Or the whole G4 is just a myth in G5 world. G5 is the only real Equestria at first time.
Macaroni C-Pony
Preenhub - We all know what you were up to this evening~

I like Theory 1, but I have another theory to add to this list which is loosely tied to the comics:
 
What if Twilight herself was responsible for the disappearance of magic, not out of failure, but in one last effort to save Equestria
 
For example: In the Transformers crossover, King Sombra stated he will always return and that even the Elements of Harmony would only temporarily scatter him and it would “only take a spark to revive him” (which is Baloney in my opinion)
 
What if, seemingly after Sombra had returned, with or without the Legion of Doom, and ganged up on Twilight. Without her friends and presumable without Discord, Twilight found herself in a situation similar to “School Daze” and rather than let the villains take control of all magic, Twilight had performed a spell or ritual of some kind leading magic to dissipate forever.
 
Not only would this permanently defeat Sombra according to his word, but it would effectively leave the Legion of Doom powerless forever. However, similar to Cozy Glow, Twilight would still have her friendships and her Kingdom. Given that this last ditch effort would the cost of her immortality, Twilight would comfort and prepare her subjects for the hard times ahead, possibly making a plan and creating a spell so that one day 5 friends would reunite to bring back the magic she was forced to sacrifice thousands of years ago…
scarasyte
My Little Pony - 1992 Edition

Blackjack
One theory I had was due to Twilight’s panic attacks when she’s overwhelmed, some pony probably used that as an opportunity to consider her unfit to lead, or even worse that pony purposely lured Twilight into a constant state of panic. Then ceasing the opportunity to take the throne for themselves. That pony would go on to be the worst leader in Equestrian history, plunging ponykind into a dark age, falling like the Roman Empire. And G5 is modernity.