Being John Malkovich is about defining human identity.
The film starts out focusing on Craig Schwarz. Gifted in the realm of making and designing dramas for puppets, Craig finds a very limited market for his talents. He is married to Lotte, a charitable woman who surrounds herself with animals from the pet store where she works. Craig recognizes the need to find a job and he applies for a filing position with LesterCorp, located on the 7th and a 1/2 floor of the Merton- Flemming building in New York City.
Craig tries and fails to woo the savvy Maxine, but outside of that, his life at LesterCorp is fairly unsatisfying. He develops a friendship with the company's head, Dr. Lester. However, things change when Craig drops a file folder behind a cabinet. When he moves the file cabinet, he finds a boarded up portal that leads directly into the head of John Malkovich, the actor. In going through the portal, Craig "becomes" Malkovich for about fifteen minutes, after which, he is deposited on the side of the New Jersey Turnpike.
Stunned with his discovery, he goes back to tell Maxine in an attempt to impress her. She sees the financial opportunity and starts to advertise the idea of "Being John Malkovich" for a fee. Craig tells Lottie that night about his new financial venture which will require him to "work late hours" because it has to take place when LesterCorp is closed. Lotte insists that she would like to try out the portal and when she does, she experiences a change in her own identity. She recognizes how much happier she was as John Malkovich than she is as Lottie. As Malkovich, Lotte finds women like Maxine desirable and tells Craig that she wants to have a procedure to make her a man. Craig tempers down her experiences as they both attend dinner at Dr. Lester's. As Lotte searches for the bathroom at one point in the evening, she discovers a room with pictures of John Malkovich at different points in his life.
Craig invites Maxine for dinner where both Lottie and Craig try to seduce her. Maxine is honest with both of them saying that she is not attracted to Craig because she needs him for their Malkovich business and then tells Lottie that she is only attracted to her when she is in Malkovich's head. Maxine leaves, with Craig and Lotte repulsed by one another.
Craig's and Maxine's business is very successful. Malkovich himself finds out about the portal and insists that it is shut down. Craig refuses and Malkovich is besides himself, uncertain as to what to do. Craig becomes disenchanted as he is rejected by both Maxine and Lotte. In Craig's anger at Lotte having sex with Maxine one night, Craig locks Lottie up in a cage and forces her to call Maxine and set up another meeting. Craig plans on entering Malkovich with Maxine thinking it's Lottie. As Craig is with Maxine as Malkovich, he learns that he can control Malkovich as he does his puppets and decides to stay inside Malkovich indefinitely.
Maxine escapes from the cage and phones Lester. Lottie learns that Lester knows of the portal and is planning on entering into Malkovich at a specific time with a group of his friends. He invites Lotte to join them. Lester tells Lottie that the only way they can enter Malkovich is through Craig leaving him. As time passes, Craig has "become" Malkovich and has parlayed Malkovich's acting career into a successful and profitable puppeteering one. Maxine stays with him, now knowing that Craig is Malkovich. However, she becomes keenly aware that she loves Lottie and is sad that she will not be able to be with her.
As the specific time approaches, Lester and his friends plan to fake a kidnapping of Maxine to force Craig out of Malkovich. Craig believes it and decides to leave Malkovich in the hope of remaining with Maxine. However, Maxine, who is pregnant with Malkovich's child and was impregnated when Lotte was Malkovich, decides to tell Lotte of her love. Lotte realizes that the child is theirs and stays with Maxine instead of going inside Malkovich with Lester and his friends.
The ending shows Lotte and Maxine enjoying their life together with their little girl, Emily, who has become the next vessel that Lester and his friends will enter at the right time. Craig's voice is heard in the distance. He has occupied Emily's body, still yearning for Maxine and a life he can never have.