A mind-blowing scene late in the film shows the puppeteer Malkovich, with Craig inside pulling his strings, operating a complex Malkovich marionette. It's made all the more brilliant by un-suspending disbelief and realizing that it's the actor Malkovich, channeling Cusack mimicking the character Malkovich, operating a puppet version of himself.

When Craig leaves the vessel Malkovich, he moves on to a much simpler life, adopting Lester's hairstyle and wardrobe and marrying Floris — who seemingly never ages. Upon their release from Malkovich's subconscious, Maxine confesses to Lotte that she is the father of Maxine's baby. Craig, Lotte, and Maxine reunite briefly on the side of the Turnpike but the women reject Craig and he vows to re-enter Malkovich and win Maxine's heart again — oblivious to the fact that he will be relegated to a passenger soul in her daughter Emily (Kelly Teacher). 

We then flash forward another seven years and see Maxine, Lotte, and Emily laughing poolside while — unbeknownst to them — Craig sits hopelessly trapped in Emily, unable to even look away from the devastating sight of his two exes living their blissful new life together.