Plot Bunny Theater: My Take on Season 9 · 4:54pm Jan 22nd, 2020
Basically at the end of season 8 Cozy Glow doesn't try to trap the Main 6 in Tartarus. Rather, she traps them in a time spell that sends them all to different timelines/universes.The same timelines we saw in Cutie Remark and a few we didn't see.
The season ends with her ascending to Alicorn and laying claim to the throne.
She also scattered Discord into six parts with the same spell across these timelines.
She figures out Starswirl's spell and gives herself a massive magical boost to force it.
As a result, it isn't a complete ascension: She needs more magic to keep going.
Luna and Celestia got drained of their magic. Cozy holds them hostage. Cadence is thus outnumbered and outgunned. But still resists as best she can with Shining.
The ultimate reveal is that another villain has been helping Cozy: Eris, who wants to take over Discord’s turf. Eris does similar things as Grogarcord did to make the villains work together, but with the goal of securing her second universe.
The next season is about the Young Six resisting the villains, building alliances, and figuring out how to make a "beacon" of sorts to help the girls find their way home. They do this by getting a hold of the last piece of Discord in their universe.. While the Main Six have to fix the problems of their timelines and ascend to alicornhood themselves. Save for Twilight, because she’s already ascended. They all have to face great trials though, as well as find the pieces of Discord in each universe, in order to get home.
The climax is that Twilight manages to get herself back home first. She works with Flash to take out Grogar's bell, which will return everyone's magic to them. They succeed but Twilight is all alone against the villains while Flash is badly injured. She moves forward to protect him, preparing for a final, useless stand… And then the cavalry arrives.
Much like the actual finale, everyone comes to help courtesy of Starlight Glimmer, Celestia, Luna, Cadence and the rest of the now ascended Main 6. And they put Discord back together again.
Eris: "... Well... Buck me."
THEN we can have an epilogue of Twilight being crowned one of six new Princesses. With the reassurance that she will never truly be alone. Yakyakistan, Griffinstone, the Changelings, the bison, the kirin, the seaponies, the Abyssians and the dragons are now all part of the Harmony Alliance and now the world is effectively at peace.Not by force of arms but through friendship and love.
And naturally, Flash Sentry is the captain of Twilight’s Royal Guard. Gallus is captain of Princess Applejack’s Royal Guard.
Probably wouldn't have been approved by Hasbro but hey, you never know...
Would've required a whole season - or at least several short movies to sort out. It is quite epic though.
This may work for the comic universe, more than anything, really. But that's just my opinion.
Apparently the original plan for Season 9 was to have a more elaborate Elements of Disharmony, and end with them being reformed, but that got scrapped, probably because they didn't want to devote so many episodes to the A plot.