Queen Chrysalis has won! Canterlot has fallen to the Changeling army and there's no longer anybody who can stand in the way of her armies! One problem, though... the Queen isn't exactly in control anymore.
Twilight Sparkle made a choice, one which has been forgiven. But she wonders whether redemption is possible. Artyom made a choice, one for which there is no redemption. But he has been forgiven. The Midnight Incident had consequences nobody foresaw.
Twilight Sparkle is an efficient pony, but there's only so many hours in the day. The obvious solution is to perform unsafe experiments so she doesn't have to poop.