Massive, Major Spoilers for other routes and later into the game...
The thing possessing Chase isn't actually Samuel, it's more of a twisted facsimile of him. An Echo (!), if you will. It's strongly implied in Jenna's route that the real Samuel survived the events of The Smoke Room in 1915, and returned to Echo only to be run over by Sidney's father and Janice, the coyote that works in the diner when they were much younger. From there I theorise the spirit that poses as Samuel latches onto Sidney's father, then onto Sidney, and finally onto Chase.
Or maybe I'm thinking too much about it and want Samuel to have a happy ending because I like him so much more than Chase.