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As incredibly bizarre and unique as Spike Jonze's Being John Malkovich is, the reality is that it was almost much, much weirder. Details about the conclusion of an earlier script have come to light online, and to call it fascinating is an extreme understatement.
This new Being John Malkovich early script info has surfaced thanks to Badass Digest, which has a fully detailed breakdown of the movie's original ending in all its weirdo glory. Beginning at about the start of the third act - which has Craig Schwartz (John Cusack) lock his wife, Lotte (Cameron Diaz), in a chimpanzee cage and leave with Maxine (Catherine Keener) to permanently take over John Malkovich's body. The big change, however, is that Craig doesn't turn Malkovich into a great puppeteer, but instead publicizes that Malkovich is a puppet and becomes famous as his controller. He gets his own show in Las Vegas, "doing scenes from On the Waterfront and juggling chainsaws."
Trouble eventually comes in the form of The Great Mantini, another world famous puppeteer who becomes incredibly jealous of Craig's success with Malkovich. He challenges the newcomer to an on-stage puppetry duel that will be judged by the puppet fan community, and the loser has to quit the business forever. The idea is that they have to perform a theatrical performance of Equis, starring Malkovich and The Great Mantini's puppet, which looks exactly like former president Harry Truman.
This is where things kind of go off the deep end. You know that group of old people seeking immortality in the movie, led by the kindly Lester (Orson Bean)? The early draft of the script actually had this group being followers of The Devil - who disguises himself as Mr. Flemmer (for whom the Mertin-Flemmer building is named). The Devil has a plan to move the old people into Malkovich and use him to take over the world - but obviously this is problematic with Craig not letting them in. This leads Mr. Flemmer to possess the Harry Truman puppet during Craig's duel with The Great Mantini, and he uses it to perform some extraordinary tricks:
[T]he Truman puppet starts juggling bowling pins while playing the psychiatrist and Malkovich has seizures, levitates and breathes fire while playing Alan Strang. The Truman puppet turns into a giant swan, which bursts into flames, and then from the ashes of the swan the corpse of the real Harry S Truman rises and implores the audience to vote for Mantini.
Craig loses and leaves Malkovich, allowing the old people access to the vessel and the ability to carry out the Devil's mission. Malkovich levitates in the air and flies out onto the streets of New York, making the world dance until they die. From there there are details about a resistance group led by Lotte and Elijay - the chimpanzee whom she has fallen in love with - and an eventual reunion with Craig. It all ends with a crazy twist ending the first suggests that The Great Mantini has long been pulling Craig's strings, but also that The Great Mantini is being controlled by strings pulled by Mr. Flemmer.
I would recommend getting all of the strange little details over at the source. According to the story, changes were made due to budgetary restrictions, and it's not hard to see why (making Malkovich fly over New York City would have been a tad bit difficult for such a small production). Would you ever want to see this version actualized, or are you satisfied with the ending that was in the film?