(please tell me if this is scary)
The water balloons with Zecora's cure for the dark water actually failed. Ponyville soon fell to the Dark Water ponies.
"We have to get out at once!" Luna said. "There's no hope for you ponies now..." somepony said. Her face was revealed to be Twilight Sparkle's face. Rainbow Dash started doing back-to-back Sonic Rainbooms, killing dozens of ponies. Fluttershy led an assault on Canterlot with her animal "friends", and she kept saying things like "Yes.... kill them all!" She then was killed by Luna. The last thing she said was "You should had loved me..." before her eyes turned completely black.
Meanwhile at Sweet Apple Acres, Apple Bloom rallied Sweetie Belle and Scootaloo to stand up and kill anypony who bullies them. They killed Applejack and Rarity, as well as other ponies. Then Sweetie Belle and Apple Bloom betrayed Scootaloo and dismembered her, each filly taking one of her wings.
With the killing of Pinkie Pie and Luna...
The Apocalypse of Equestria had begun.
To be continued...