I'm going to avoid all the details mentioned by the noder above, and get straight to the good stuff. That said, this node is going to be made entirely of !!!spoilers!!!, so if that scares you, skip this.
Adaptation is a fine movie, but it's very convoluted and confusing. It's not told in chronological order. It's a movie about a guy making a movie, and you are watching him write the script for the movie you are watching. Confused yet? Sadly, this movie is very fine indeed, but it never really manages to escape being merely interesting, owing to this and its ending.
Let's start at the beginning before we talk of the end. Charlie Kaufman has to write a movie. Charlie Kaufman can't think of ideas. Charlie Kaufman is fat, bald, and ugly, and reminds himself constantly of this. He's also intelligent, yet he lives with Donald Kaufman, his doofus brother. Now the pathos. Cut to scene of Charlie on the set of "Being John Malkovich"; the actors are all together talking and enjoying themselves; Charlie sits in a corner by himself. His lovable brother Donald comes in, embarasses Charlie, and a week later Donald is hobnobbing with all of the actors who ignored Charlie. Donald is also dating an attractive makeup artist from the set of the movie; the woman Charlie is interested in now has a boyfriend.
Charlie's still failing miserably at writing his script when Donald decides that he too should become a movie writer. Donald is going to a class on movie writing, held by a man who claims to have figured out the formula that guides classic movies and now teaches his students how to replicate this formula in their own movies. Charlie says that what that man teaches is formulaic and a stifling of the creative process. Donald ignores him. Donald writes a cliched story about a killer with multiple personalities. Donald makes millions. Charlie is still struggling with his script.
As part of a last ditch effort to write an ending to his movie, Charlie goes to the workshop his brother went to, meets this man, and decides to abandon the creative process and follow this man's ideas. Here's where the satire begins, and this satire seems to be either Kaufman's private joke on how moronic he thinks his audience is, or on how his audience has no taste, and as a result the irony is so subtle most people will miss it.
Remember, Charlie is writing this movie as you watch him. So he writes some clichéd Hollywood nonsense in accordance with the advice from the man who runs the workshop. Remember Susan Orlean, the New Yorker writer doing an article on John Laroche? She's really in love with Laroche, and she also turns into a raging drug addict. Charlie needs to find out if this is true, so he goes down to Florida following Susan Orlean to see if she really is having an affair. She is. Now this movie slips into the absurdity that is difficult to catch because Hollywood revels in such things.
Charlie is caught prowling around Laroche's house late at night while Orlean and Laroche are getting stoned. Laroche takes him inside, and Orlean demands that they kill Kaufman. Chase seen ensues, cut to the thrilling climax where Laroche is pointing a gun at Charlie;Charlie is saved at the last minute when an alligator devours Laroche!!! Cut to cheesy romantic epiphany, cut to feel good ending, hurray for satire.
This movie had great potential. Instead it becomes Kaufman's rant against the movie industry and life in general; he feels that those who sell out (in the case of the movie industry) and idiots in general (in the case of life and the movie industry) succeed while the true geniuses suffer. His own main character suffers until he sells out, not only in the movie industry but in life; his own main character who is supposed to be him. You could take it as tragedy I suppose in which our stoic hero finally gives in, but I expected better from Kaufman than an ending that was merely a joke; I suppose he gets the last laugh because his movie will do well because he sold out. This movie is pretty good, "Confessions of a Dangerous Mind" is better.
A noder who wishes to remain anonymous made a good point. The Orchid Thief is a book about obsession, and this is important because Charlie can't find it, because obsession is ultimately not real life. He wants to write a movie about normal life with no car chases or anything; he realizes this will not sell so he throws in an action scene at the end and a convenient ending that ties up all the knots. He adapts, hence "Adaptation"; all life must adapt or be lost to history.
A few people have also messaged me about the ending to this movie. My thoughts: you can either say he adapted, and learned to live with not being able to date the woman he loves, or you can say it was part of the cheesy romantic ending. I'm starting to learn towards the adaptation explanation, because it seems too deep to be merely a cheesy romantic ending. You decide.