Craig (John Cusack) is a puppeteer who takes a new job as a filing clerk. He's married to Lotte (Cameron Diaz, Things You Can Tell Just by Looking at Her) but has the hots for co-worker Maxine (Catherine Keener, Your Friends and Neighbors, If These Walls Could Talk I).

This is a bit hard to explain, but Craig finds a hidden door at work that turns out to be a portal into actor John Malkovich. For fifteen minutes, you see the world as John does, before you get spit out on the New Jersey Turnpike. Craig and Maxine work on selling tickets to the ride.

From her experiences as John, Lotte decides that she may be a transsexual. "For the first time, everything just felt right." She really wants to BE John Malkovich. Maxine (who has no interest in Craig) is turned on by the idea of Lotte inside John's head. She meets John for a date while Lotte is inside him, and for the first time, Lotte is attracted to a woman. Maxine later tells her that she is "smitten with you, but only when you're in Malcovich. Behind the stubble and the male pattern baldness, I sensed your feminine longing."

Maxine goes on another date with John and puts off his advances until she can sense Lotte inside. Craig begins to snap when he realizes that his wife and love interest love one another, and he enters John the next time Lotte is supposed to be there.

John begins to sense that someone is controlling his voice and actions, and he and his friend Charlie Sheen surmise that Maxine is using John "to channel some dead lesbian lover." Craig the puppeteer begins to control more of John's movements and voice and takes him over completely.

The reason for all of this portal business is too complicated to explain, but all ends well. Craig leaves Malkevich's body. Maxine is pregnant and keeps the baby because Lotte is the father, and we finally see Maxine and Lotte kiss in their own bodies. They raise their daughter Emily together.

A very odd, yet fascinating, film.