This story is a sequel to Pinkie Pie’s Clone Wins a Game of Hide-and-Seek
Princess Twilight Sparkle helped Pinkie Pie clone herself to finish a giant gingerbread castle in time for the Gala. Twilight's going to find out which Pinkie Pie clone, with science. But somepony isn't happy to be pulled in as Twilight's research assistant.
This story can easily be read without reading the prequel.