A teaser released on Twitter gives a few clues, which you can hear if you "listen closely".
This is not the first time a series has gone with a new story idea for each season.
The horror series American Horror Story, which already has eight seasons, feature new characters and storylines for each season.
The first season of Hill House follows the Crain family after they moved into an old mansion filled with ghosts and other paranormal activity.
It shows the Crain siblings in two different eras of life, when they were young and as adults.
The show starts Michael Huisman, Carla Gugino, Henry Thomas, Elizabeth Reaser, Timothy Hutton, Victoria Pedretti, Kate Siegel and Oliver Jackson-Cohen.
Flanagan previously told EW that "the story of Crain family is told. It's done," which is why they are going for a new story line in the next season.
"I think that there are all sorts of different directions we could go in, with the house or with something completely different. I love the idea of an anthology as well. But to me, I felt like the Crains have been through enough, and we left them exactly as we all wanted to remember them, those of us who worked on it.
"We toyed with a cliffhanger ending and we toyed with other ideas, but ultimately, in the writers' room and with the cast and everything else, we really felt like the story demanded a certain kind of closure from us and we were happy to close the book on that family," he said.