So you see, one day in the far future, Sophie and Agatha decided to invent time travel. They went back into Once Upon a Time to a Long Long Time Ago. There were no School Masters in those days, so Sophie and Agatha decided they would become them.
Now the School Masters were dudes, and Sophie and Agatha were dudetts, so they went to the gnomes for help.
Now securely the School Masters, they started the School for Good and evil. You'd think that with Agatha as good, and Sophie as evil, Agatha would become School Master Rhian, and Sophie would become School Master Rafal, but they decided to shake things up a little and swap roles.
Now the rest is history. Rafal killed Rhian and took over the world.
It truly has been Agatha all along.