When Craig Schwartz, a washed-up puppeteer (John Cusack), is forced to take an entry level job to make ends meet, he discovers a secret passageway in his office that leads into the mind of John Malkovich (who plays himself). After 15 minutes in Malkovich's consciousness, Craig is spit out onto the side of the New Jersey turnpike. However, the exhilarating titillation of "being John Malkovich" incites him to share his new-found finding with his wife (Cameron Diaz) and his co-worker (Catherine Keener) who both enter the portal as well. The two end up falling in love and use Malkovich as the middle man.

Once Craig figures out how to dominate Malkovich more and more, the actor decides to enter himself.