The ending is a simulation in Sister Paxton’s head:
“Sister Paxton is dying on the floor, praying, Sister Barnes has been dead since Mr. Reed cut her throat, and the final scene is just a simulation of Sister Paxton’s head. Like what the three of them discussed about the prophet’s revelation, the brain just sees what it wants to see before dying.
In the case of Sister Paxton, she imagines some sort of divine justice: Her friend is miraculously still alive, just in time to kill the monster (Reed). Paxton manages to stop the internal bleeding of her cut and manages to get out of the basement, find a way out of the house, and finally sees a butterfly posing on her hand. As in a way to see the light, then, at the last second, disappears, breaking the illusion.”