While we have not heard any things about Queen Chrysalis or King Sombra showing up. With comment from staff said that they may show up but not as we expected to be.
Which beg the question what are not expected to show. Here theory on what meant when Starlight Glimmer going to do alternant time line event. We going to see two major villian Chrysalis and Sombra but the here kicker when Twilight meet those two surprise how out of charater this would shock her. That they would rather help Twilight then to hurt her. But would you guys think about this?

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but the here kicker when Twilight meet those two surprise how out of charater this would shock her. That they would rather help Twilight then to hurt her. But would you guys think about this?

A badly-written bad idea.

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In reality, I think it's more like a Ripple Effect-Proof Memory situation; it already has been revealed that Starlight Glimmer goes back to prevent Rainbow Dash's Sonic Rainboom from ever happening and getting their cutie marks, but maybe Twilight realizes not everything's right and goes to hunt down the others, restore their memory, and go straight to Starlight without the other villains appearing.

Doing all that by itself in the 2 episodes would be hectic, and honestly having the other villains come in would make things even more rushed. Also, otherwise can simply be explained by the time travel effect not going back that far for Sombra and, if my scenario is true, Chrysalis wouldn't even have been known to the mane 6.

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Here something else would Twilight herself forget lose her memory from true timeline?

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Again, with the Ripple-Effect Proof Memory thing, Twilight would probably be the only one not to lose her memory of the original timeline.

4828232 If your theory true. then the writers could more or less have salute to both Chrysalis, and Sombra. By having Twilight see a glimpse of the Alternate timeline. And being the fact without the Mane 6 and Spike, then their plans would perfectly. Meanwhile Discord would mostly be some where off scream causing havoc. And the only villain I see not being around in this Alternate Timeline would be maybe Nightmare Moon, give my own theories on her return. However she maybe back as well.

Now given the background of these villains. Then timeline would show Twilight, a world in Chaos, Currently being Co-Ruled by King Sombra and (Queen) Nightmare Moon, and they are constantly at war with Queen Chrysalis.

Now I doubt any shipping would going between the two Co-Rulers, it just those two would have very similar plans(Eternal Night, Eternal Darkness) so it would make sense for them to rule along side each other, and it would very much clash with Queen Chrysalis own plan(Consume All Love to feed her Changlings)

4828213 I think your Idea may work but only for Chrysalis, being that the Alternate Timeline would be bad for her Changelings. The best way Alternate the Timeline would be to prevent the Sonic Rainboom. In doing so all of the Villains thought the series would be free, without the Main 6 to stop them. It would be a world (most likely ruled by Sombra) without love, so no food for the Changlings.

So yeah I could see Chrysalis working with Twilight. But not Sombra, for he would already have what he wanted(Eternal Darkness) thanks to Nightmare Moon. I am think maybe he will be the Villain. And once Starlight Glimmer realizes how much she has change to timeline. Then she would(probably near the End) try to help to fix it.

This would make for the best season finaly ever.

4828484 yeah but the problem is unless they decided to make it the first Three part finale (they have ever had). I am worried they would either rush it or leave out a few details, just to make it a two part finale

4828232 EW! All those paradoxal, broken time mechanics!
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