According to writer Charlie Kaufman, his original idea for Being John Malkovich started as nothing but a story about a man who falls in love with someone other than his wife. He slowly added details as time went on, including things like the 7½ floor of the Mertin Flemmer Building, and a stranger aspect to the romance of the film. Despite these developments, the idea of John Malkovich (or any other similarly positioned actor) being the object of the romance was not introduced until years after the idea for the film was born.
Kaufman completed the script for the film in 1994, and sent it out to a large number of production company and film studio executives. Though many of them agreed that it was good, none of them wanted to take on the project. In a moment of desperation, Kaufman sent the script to the world-renowned director Francis Ford Coppola. Though Coppola ultimately decided to pass on directing the film, he passed the script on in 1996 to his then son-in-law Spike Jonze, who agreed to direct the film by early 1997.
It is Jonze that gave life to the film. Shortly after agreeing to be the director, he brought the project to Propoganda Films, who, based on previous partnerships with Jonze, agreed to produce the film alongside the production company Single Cell Pictures. It was during a conference in which Jonze was trying to gain funding when the idea of placing John Malkovich (or another famous actor in a similar position). He soon after proposed the idea to Malkovich himself, and he quickly agreed.
At a point after Malkovich accepted the project, one producer asked him why it had to be Malkovich instead of someone else. Malkovich responded that if the movie was good, he had a chance to be forever associated with a great movie and an interesting, positive character. He said that the chance of this outweighed the possibility of the film being terrible and hurting his reputation. Director Spike Jonze also strongly believed that he was the best possible actor for the role and would have to be hard pressed to alter this belief and casting decision.
In casting, Jonze personally selected and gave input on much of the cast. He wanted the film to turn out as much like his vision of it, and that in order for that to happen he needed to have substantial influence on every part of the process.
In the end, the film turned out to be a success among critics and viewers alike (though not at the box office), much in part because of the exceptional directorial decisions and actions of Spike Jonze.