This is my take on what might have happen after The FNaF Book:The Twisted Ones. It's a real good book btw you should seriously consider reading.
Having trouble with her memories, Charlie is left confused with herself. Along the way, she slowly loses control of herself after being exposed to the thing she had dread for quite a while. Fueled with murderous intent, she goes on into town with another user in her head.
After the Black Mesa Incident, portal storms erupted all across the world. Not only did the Humans let the Xen species in, they let in a stronger force. A multidimensional empire called The Combine. They conquered many planets across many galaxies. And we were now one of them. [Loosely based of Half Life 2...