Equestria is expanding unstoppably. The Conversion Bureaus are working at peak capacity. It looks absolutely certain that Celestia will replace humanity with ponies.
But then one niggling flaw appears in her plan. You see, humanity's religions, while dismissed by Celestia as just more evidence of human barbarism, are correct in at least one respect. Humanity has a loving father, and what Celestia is doing makes Him angry. So angry in fact, He's going to do what He hasn't done since ancient times: smite.
Seems like Exodus is being reenacted, and guess who's playing Pharoah?