So this is kinda the universe, where sombra took over. But I'm taking it a little farther, so the mane seven (including starlight) already have kiddos, and then Sombra comes back, takes over, and here we go.
Twilight Sparkle:
Before Takeover:
Married to flash sentry
had 3 children
Taught magic
AFTER TAKEOVER:
Helped start the rebellion
Flash was killed by Sombra's army while trying to protect twilight
She was separated from her kids
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Applejack:
BEFORE TAKEOVER:
Married to Flam
Had 2 children
Ran sweet apple acres
AFTER TAKEOVER:
Works as a food supplier to the rebellion
had another foal
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RAINBOW DASH:
BEFORE TAKE