The film was nominated in the 72nd Academy Awards in three categories: Best Director for Jonze, Best Original Screenplay for Kaufman and Best Supporting Actress for Keener
PlotCraig Schwartz (John Cusack) is an unemployed puppeteer in a forlorn marriage with his pet-obsessed wife Lotte (Cameron Diaz). Gaining a file clerk job through Dr. Lester (Orson Bean) at LesterCorp, in the strange Floor 7½ low-ceiling offices of the Mertin Flemmer Building in New York City, he develops an attraction to his co-worker Maxine (Catherine Keener), who does not return his affections. Craig discovers a small door behind a filing cabinet which he enters, finding himself in the mind of actor John Malkovich; able to observe and sense whatever Malkovich does for fifteen minutes before he is ejected and dropped into a ditch near the New Jersey Turnpike. Craig reveals the portal to Maxine and they decide to let others use it at $200 a turn.
Craig tells Lotte, who becomes obsessed with the experience, allowing her to live out her transgender desires. Lotte becomes attracted to Maxine and they begin a sexual relationship by having Lotte inside Malkovich while Maxine has sexual intercourse with Malkovich. Craig, forsaken by both women, locks up Lotte in a cage. Unbeknownst to Maxine, he then enters into Malkovich's mind and has a sexual encounter with Maxine. Drawing on his puppeteering, Craig discovers that he is able to control Malkovich's actions while in his head, causing the actor to become paranoid. After consulting with his friend Charlie Sheen, Malkovich trails Maxine to the Mertin Flemmer building, where he finds and tries the portal and is placed in a world where everyone looks like him and can only say "Malkovich"; he is ejected and meets Craig by the turnpike, and angrily demands that the portal be closed, to which Craig refuses.
Lotte escapes and phones Maxine, revealing that Craig was having sex with her. Maxine is annoyed but accepts it as she enjoyed the experience. Seeking help, Lotte finds Dr. Lester, who reveals himself to be actually Captain Mertin, the creator of LesterCorp; he is well aware of the portal and has a room dedicated to Malkovich. Lester explains that the person connected to it becomes "ripe" for occupation on the eve of their 44th birthday. However after turning 44, the portal moves to its next host, an unborn child. The former allows one to increase their life before moving on to another host while the latter means being trapped within the unborn child. Dr. Lester, who has been using the portal to prolong his life, reveals his plan to use Malkovich for himself and several of his friends. Offered the chance to join Lester's group, Lotte warns him that Schwartz has control.
Meanwhile, Craig finds he is able to remain in Malkovich indefinitely. He spends the next eight months in Malkovich's body and through his control, turns Malkovich into a world-famous puppeteer, revitalizing puppetry. Malkovich also gets married to Maxine and learns that she is pregnant, as their relationship grows distant. Malkovich's 44th birthday approaches so Dr. Lester and his friends cut a deal with Maxine and fake a kidnapping, they call up Craig threatening to kill her if Craig does not leave. He shuts the phone down out of remorse causing Dr. Lester to think that he had called their bluff. Lotte loses hope and attempts to kill Maxine, but they end up at the turnpike after falling through the portal and Malkovich's shame-ridden subconscious. Maxine reveals that she conceived when Lotte was inside Malkovich's body, and kept the child because it is theirs. The revelation cements their love for each other.
Eventually, Craig calls back Dr. Lester thinking Maxine is still in danger, realising his opportunity Dr. Lester continues his bluff and convinces Craig to leave Malkovich's body voluntarily in his hope to win Maxine back. Malkovich finds that he has regained control of himself but his joy is cut short as moments later Dr. Lester and his friends enter the portal. Craig, discovering that Lotte and Maxine are together again, enters the portal in an attempt to become Malkovich and regain Maxine, but is too late and finds himself in the next host: Emily, the baby of Maxine. Craig is permanently imprisoned and must now spend the next 40 years watching Maxine and Lotte live happily ever after through Emily's eyes. Later, an aging Malkovich, under the collective mind of Dr. Lester and his friends, reveals to a now aged Sheen a plan to prolong their lives through Emily.
