There are few films as anomalous as Being John Malkovich. On paper the movie itself should be insufferable - the story of a man who enters a portal into the mind of actor John Malkovich, gets involved in a love triangle with transgender implications and runs afoul of a cult intending to use Malkovich as their vessel for immortality sounds so unbelievably over-quirky that just typing this synopsis irritated me - but the actual film is funny and smart and avoids being quirky by being tongue-in-cheek and manages to be profound and effective in every way. It's a movie that shouldn't be any good, and it launched the film careers of two men who shouldn't be making the movies they make: Spike Jonze shot music and skate videos and writer Charlie Kaufman had done some episodes of Ned and Stacey. Neither of these guys were obvious choices to make a movie that helped redefine what an arthouse picture was, but fifteen years later we're still marveling over how good Being John Malkovich is.

Would we still be marveling if Kaufman's original ending - scrapped for budgetary reasons, among other things - made it to the screen? I remember getting my hands on this early script right around the release of the film and being boggled by the huge differences between it and the final product, and the fact that Kevin Bacon was Malkovich's actor confidante (it's Charlie Sheen in the finished film) is the least of the changes.

Here's where the main divergence happens: Craig (John Cusack) has taken control of Malkovich (John Malkovich) and run off with Maxine (Catherine Keener). Lotte (Cameron Diaz) is locked in the cage with Elijah the chimp. Lester (Orson Bean) and his friends are horrified to find their plans being thwarted.

In the original script Craig Schwartz takes possession of Malkovich and remains within him for months - just as he does in the movie. But in the script Craig doesn't make Malkovich a famous puppeteer - he makes Malkovich a famous puppet. Craig declares himself the man controlling Malkovich, the world's most complicated puppet, and he embarks on a one-man show at the Luxor in Vegas that includes Malkovich doing scenes from On the Waterfront and juggling chainsaws.

Meanwhile, it turns out that the group hoping to live in Malkovich are being led by the actual Devil himself, in the guise of Mr. Flemmer (the man after whom the Mertin-Flemmer building is half-named). The Devil hopes to get his group into the vessel and use it as a tool for evil - they will rule the world together in the body of Malkovich. But first they have to get Craig out of it. Flemmer comes to Craig in a dream, telling him he must vacate the vessel, but Maxine, who is Craig's producer, tells him that's crazy talk.

Then Craig is visited by The Great Mantini, the world's best puppeteer. He is famous for his giant Harry S. Truman puppet (not to be confused with his giant Robert Morse puppet (yes, Bertram Cooper from Mad Men), which starred in Tru, a puppet biography of Truman), and he can't stand the acclaim Craig has been getting for his flashy Vegas show. So he challenges his rival to a duel - the Malkovich puppet and the Truman puppet will act together in a production of Equus and the puppet fanbase will decide who is the greatest puppeteer. Whoever loses will retire forever from puppetry - Craig will have to leave Malkovich.

When Flemmer gets wind of this he teleports to the theater (freezing Charles Nelson Reillly in time along the way) and takes control of the Truman puppet during the second act of Equus. The first act was a total bore (during intermission a theatergoer complains that the Truman puppet is wooden), but once the Devil takes over everything kicks up a notch. And when I say kicks it up a notch the 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.

That does it - Mantini wins. Craig, depressed, leaves Malkovich and is ejected onto the side of the turnpike. Flemmer and his cultists jump into the tunnel and take control of the vessel; Malkovich is now fully powered and hovers over the crowd in the theater, telling them they are now his lowly subjects. He floats into the streets of Midtown Manhattan and forces the crowd into an intricate dance number, driving them to dance until they begin to drop dead one by one.

Meanwhile Lotte and Elijah the chimp have been on the run. Elijah has learned sign language, and they were trying to warn Craig that leaving Malkovich would open the door for the Devil, but it was too late. Now, as Malkovich takes over the world and turns it literally grey, they are hidden in a small oasis of color in Central Park. They lead a small resistance group - and they're in love. But Lotte feels like she has to stop Malkovich, and she's going to smuggle a bomb into the tunnel and blow him up from the inside.

As she heads to the Mertin-Flemmer building Lotte runs into Craig. They talk. She tells him she's in love with one of the animals (he guesses an iguana), and he concedes that Elijah is a better man than he is. When Lotte tells him about her plan but he explains that the portal has been closed exactly to thwart any attempts like this. Lotte looks on the bright side - her community needs another farmer. Craig can come back with her. "Yes, show me where you live," Craig says, putting his arm around his ex. And we see that there's a thin wire on his arm, and the camera pans up following the wire and we see that The Great Mantini is controlling him. But there are wires on his limbs as well, and the camera follows those further up, and we see Flemmer controlling Mantini. And Flemmer laughs and the camera dives into his mouth, and the throat looks just like the tunnel to the vessel...

The end.

The final puppet battle and the forced dance sequence have haunted my dreams for the last decade. They're such evocatively weird moments, and clearly too expensive for the movie that got made. Keeping them in would have made Being John Malkovich a totally bizarre trip out movie, but removing them allowed Being John Malkovich to be an actually human story with an ending that is unsettling and powerful - Craig is trapped inside the soul of the next vessel, now just a baby. There's a Twilight Zone quality to the final ending that's satisfying and feels like a commentary on the ways we are living our lives through other people, becoming passive observers of life instead of participants.

But that original ending! The madness of Harry S Truman himself showing up! Malkovich juggling chainsaws! Lotte and Elijah sharing a passionate kiss! I'd like to slip briefly into the alternate world where that movie got made just to see what the hell it was like.