‘Aatma’ revolves around a woman, who finds her and her daughter's life in danger after her past comes haunting! What follows is a single mother fights who against the supernatural in order to hold on to her daughter. It starts off with Nia, daughter of Maya (Bipasha Basu) and Abhay (Nawazuddin Siddiqui), who are divorced. Maya and Nia live with Maya's parents. Nia is unaware of the fact that her father is dead. Maya deliberately hides the truth from her as Nia is a sensitive child and worships her father. Things start getting bizarre when Paras, Nia's classmate who bullies her, ends up dead. Soon after, Nia's teacher, Mrs. Sinha, who complains about Nia, is also found dead. Moreover, Nia starts talking to her absent father.

Concerned about the absurd change in Nia's behavior, Maya takes her for counseling. It is revealed that Abhay was a hot-tempered man. He loses his job and friends because of his frequent violent bouts of anger, and also suspects Maya of having an affair with a colleague. However, he loves his daughter more than anything else. After Abhay starts beating up Maya, she files for divorce and gets the sole custody of Nia. Abhay cannot bear this and threatens Maya that he will take Nia away from her. Shortly after the hearing, Abhay dies in a car accident. After the session, the counselor (Mohan Kapoor) advises Maya to take Nia out for the weekend. The mother daughter duo does so but Abhay possesses Nia and tells Maya he will take their daughter.

Maya consults a priest (Darshan Jariwala), who tells Maya that as long as she and her daughter share a strong bond of love, Abhay won't be able to kill either of them. After the counselor tries to convince Nia that her father is dead, the counselor himself is found dead. Later, Abhay kills Maya's friend and frames Maya, who is admitted into a mental health facility. Maya's mother calls the priest home to get the home blessed. Abhay kills the priest and Maya's mother. Maya, in a desperate bid to save her daughter, kills her, as she remembers the priest's words that no mortal can fight a spirit. Maya becomes a spirit and saves Nia just as Abhay is about to kill her. She also destroys Abhay's spirit, thus ensuring Nia's safety for the rest of her life.