Orphan takes place in the abandoned Sheppard's Orphanage in Silent Hill, Maine. One mysterious night, thirty years ago, almost every child in the orphanage was murdered, except for 3 children: Ben, Moon, and Karen. The game is divided into three chapters, one for each character, which interlock each other, shedding some light on the events that took place thirty years before.
The game begins with the player controlling Ben, who was one of the few children that survived the murders at the orphanage. Thirty years later, Ben returns to the Sheppard's Orphanage to see how things are doing. As he explores the orphanage, he hears the cries of another person, Karen, through a ventilation duct and he offers to find and release her as she can't remember how she got here. Soon, he finds a strange red symbol (Halo of the Sun) in a disused bathroom that transforms the orphanage into a grotesque, bloody Otherworld version infested with monsters. In the orphanage, Ben finds a letter stating that he was diagnosed with cancer as a child. A voice calls him to the shower room, his safe haven when he was a child. He returns to the shower room and is killed by an unseen force.
After Ben's scenario, the player switches over to Moon, another orphan that survived the massacre. Moon had attempted suicide since she was three years old and her parents, tired of her desperate attempts, brought her to the orphanage. Thirty years later, she returns to the orphanage and discovers Ben's corpse in the shower room and is told to kill herself by the same voice that Ben encountered. After further exploring, she obtains some scissors and the voice tells her to use them on herself. Instead she uses them to solve a puzzle, after which she discovers a suicide letter from herself to her parents, which Moon apparently never wrote. When Moon enters the boy's washroom, her apparent suicide location in the letter, she encounters the voice again who reveals herself to be Alessa. Alessa tells Moon not to fear her and that Moon needs to "feel this." Moon tells Alessa to get away, and the chapter ends on a cliffhanger.
After Moon's scenario, the player switches over to Karen, who is locked in the storeroom with no means of escape. She hears a voice through the ventilation duct (Ben) who offers to help her. She then rests on the floor and falls asleep. When she wakes up, the door is open and she finds Ben's corpse in the nearby shower room. As Karen explores, she regains fragments of her memory from the voice; Karen has a deceased sister named Alessa, who is the strange voice. After obtaining a drawing and solving a puzzle, Karen gains entry to a room in the Otherworld where she encounters Alessa, who helps her regain her full memory. It is revealed that Alessa wanted revenge for being put in the orphanage and manipulated her sister, Karen, into murdering all the people in the orphanage. Karen did so and grew up not knowing the truth, hence she forgot. Karen tells Alessa that she didn't want to kill and that Alessa was the one who made her do it. Alessa then thinks Karen is turning on her and unleashes a monster. After Karen kills it, Alessa tells her to "Visit Moon. She's waiting..."