Behind Jon Cusak’s filing cabinet is a portal to the mind of John Malkovich. You experience everything that Malkovich does from Malkovich’s mind. You have no control over him, you just see what he sees. This lasts for only about 15 minutes, then you fall from the sky landing just off the Jersey Turnpike.

Cusak’s wife (Cameron Diaz) enters the portal and experiences life as Malkovich. She decides it was so natural that she must really be a man. While she is in Malkovich's mind, he (and she) have sex with Cusak’s coworker Maxine. Maxine becomes pregnant from this encounter. A jealous Cusak, who has been lusting after Maxine, even though she wants nothing to do with him, discovers that the only way he can have sex with Maxine is to enter Malkovich’s mind and have sex with her as Malkovich.

It seems that Cusak is an expert puppeteer and discovers that he can control Malkovich for as long as he wants. He stays Malkovich for a couple years, marries Maxine and they have a daughter.

He, as Malkovich, quits acting to become the worlds greatest puppeteer.

Maxine is actually in love with Cameron Diaz, not Malkovich. She kept the baby only because she knew that Cameron was in Malkovich's mind when it was conceived.

Cusak is forced to leave Malkovich’s brain because the portal actually belongs to his boss, Orson Bean. Yah, the “what’s my line” guy.

Maxine and Diaz want nothing to do with Cusak. They live the rest of their life together as a couple, raising “their” daughter.

The portal now is the portal to the daughter's mind which Cusak now occupies.