Being John Malkovich had a few scenes that weren't filmed. For instance, there were a couple of extra
orientation videos on certain
subjects, such as the
small door and
John Horatio Malkovich. Then there was
thirty minutes or so worth of an
original ending that was changed due to
budget considerations. But it's still preserved in the
original screenplay, which is up on Drew's
Script-O-Rama.
Basically it veers off from the point where Craig is inside Malkovich and using him to do the same puppeteering work at the beginning of the movie as a demonstration for Maxine. Craig gets the idea to let everybody in on his controlling by showcasing Malkovich as the world's most complicated puppet. It also serves a way for Craig to get the upper hand on Derek Mantini, who he was jealous of.
Now some of the original points stay in. The agent meeting, Craig/Malkovich's rise to puppeteering fame, and Lester's revelation tht he's Captain Mertin. But the details about getting in before Malkovich turns 44 are cut, not like it matters.Anyways, the new aspects introduced are the introduction of Mr. Flemmer, a bigger role for Mantini, and Lotte breaking away and attempting to stop the Mertin cult on her own. It drags a little more, and tends to go back to the sophmoric humor from the first part of the film, but leads up to a final duel between Craig/Malkovich and Mantini (with his Harry S. Truman puppet} in a production of the play Equus, where the crowd decides the best puppeteer and the loser quits the business.
The actual events that go down during the play would end up requiring a quite a bit more in the budget for special effects, due to some of the tricks that "Mr. Flemmer" pulls. And the ending is totally bizarre, with the Mertin cult controlling Malkovich as a wicked king reigning over all of humankind, Lotte hiding out in a camoflauged area of Central Park and getting married to Elijah (the monkey), and Craig...well...the image that the original ending would have provided would have been one of the eeriest ever.
If you don't wanna go through the Script-O-Rama maze, then you can go to http://www.godamongdirectors.com/scripts/bejomalk.txt. It's quite a treat to read.