Vincent is the playable character at the beginning and end of the game. He explores a mansion where he finds a room with butterflies on the wall and, "a photo of a family, the parents and their two girls... Karen and Alessa's family". The clocks in the mansion have all stopped working since "the accident" 40 years before, a fire that Vincent started, leading to the events at the orphanage. It flashes back to Vincent's childhood, where his father, Gary, told him to become a firefighter. He is upset and sets a fire. Alessa's sister, Karen, created the monsters in the game by murdering children in the orphanage 40 years ago. The monsters begin to appear in the normal world, showing that Karen has become more powerful than before. When Vincent goes to the dining room of the mansion, he is attacked by the evil side of Karen that leaves him dying.
In the middle part of the game, Emilie becomes the playable character. Emilie wakes up in an abandoned mansion in the Otherworld with no memory of how she got there. Emilie hears a voice who tells her "you need to save it" and "is dying". Upon waking she is attacked by one of the creatures that roam the place, and after the fight she hears the voice of Alessa, who sends her to kill all the monsters. After a series of struggles Emilie then hears the same voice telling her to return to the real world. After a shift to the real world, Emilie wound up in a dining room, where she once again hears the voice of Alessa and then the two converse. During the conversation Emilie hears a groan (Vincent) and questions Alessa about it to which she replies, "That's the man you must save". After asking how, Emilie is instructed by Alessa to suicide using a holy knife found previously in the mansion. Emilie refuses at first, but Alessa reveals to her that all of the monsters killed earlier were created by Karen from the spirits of children killed in the massacre and that when Emilie killed them they met in her body. If she were to suicide it would release the spirits, allowing them to revive Vincent. Emilie still refuses, but agrees when Alessa says this is the only way she can "get out of hell" and that if she did not, other innocent people would end up dying.
After Emilie's death, Vincent becomes the playable character again. Alessa reveals herself to be the "evil part of Alessa." The murders at the orphanage were done to "wake her up." She kept Vincent alive so she could use him to kill Karen. At the end of the game after killing the evil side of Karen, Vincent begins to have a heart attack and talks with Alessa one last time before he dies. She tells Vincent that the real purpose of the massacre of the orphanage was to "wake up your spirit" and for that she needed to "wake up" all orphans of Sheppard's Orphanage.
The evil side of Alessa remained alive after Alessa's death, and to be able to rest in peace she would have to fulfill the promise she made to Karen that she would "clean up all the evil of the orphanage", killing all the orphans of Sheppard and that she would "find a better place to live with Karen". Once she did the massacre, she was just stuck in the Otherworld (referred to "hell") as punishment and also failed to fulfill the promise because the orphans Moon, Ben, Karen and Emilie have survived. After killing all orphans, including the evil side of Karen, Alessa finally manages to free her spirit from hell together with the orphans (including the good side of Karen) of the hell. In the process, the evil side of Karen, the evil side of Alessa and Vincent go to the hell because they were really responsible for the incident.