This is a sequel to Rainbow Factory by AuroraDawn, My Little Dashie by ROBCakeran53, and Rocket To Insanity : Twilight's Passage by DontWakeTheNeighbour (after chapter 7: Spread). All those stories are in the same universe as this story
When Twilight Sparkle finds a way to bring her friends back to life, the mystery antagonist will stop at nothing to break the pony’s hearts. His partner will go as far as to attack Rainbow Dash’s human father who hasn’t seen her in 20 years, create an infection that is even more evil then the last, and bring back something that Princess Celestia thought she had banished from the very space time continuum…the Rainbow Factory. Hope begins to diminish as Rainbow’s dad loses his humanity and becomes an enemy, Pinkie slowly looses her mind and becomes pinkamena, and Equestria is taken over by darkness. Killing or banishing the antagonist may not be something Celestia is willing to do when the villain’s tragic back story is revealed and all hope in saving Equestria lies in his hooves alone.

This story is told in 4 arcs

Arc One: Revenge

Arc Two: The Human King of Crime

Arc Three: All Hail the Pink Queen

Arc Four: The Final Fight for Equestria

Arcs one to three take place after season two. Arc Four takes place after Season 3 episode 10: Keep Calm and Flutter On