So what does one make of a film like Naked Lunch? First, it's based on the book by William S. Burroughs, hardly a positive sign if you're trying to figure out what the hell's going on. Second, the film is directed by David Cronenberg who isn't exactly a mainstream blockbuster film maker and isn't going to make things any more clear. The combination leads to an obfuscated story which can be interpreted many ways (like many artsy films). In the end, it's enjoyable purely for its vivid tripped-out psychedelic and surreal imagery, and is probably the reason it has gained cult status.
The plot starts with William Lee (Peter Weller), a recovering addict who has turned to writing pornography to make a living. High on "bug powder", he shoots his wife after failing to play a game of "William Tell" successfully. What happens next is anyone's guess, even if you've watched the film a dozen times.
Movies like Naked Lunch are messing with your mind. The whole film, particularly in the end, never really makes sense. While some of us have a tendency to want to figure it out, it's important to realise that it may simply not be worth it. The film has many levels to it: one one level, it's an analysis of what could happen in a hallucinatory drug use/abuse situation. Perhaps everything that happens after Lee kills his wife accidentally (just as Burroughs himself did) is just a form of drug-induced psychosis (imagined or real).
Perhaps there really is an X Files type alien-conspiracy going on here, involving the Interzone region (where Lee flees to) and Annexia. The warring aliens take on the form of typewriters in two different forms: cockroaches and alien-looking monsters who spew out goo. The Interzone reason is an Arabian city of sorts where an ample supply of hedonistic pleasure is available.
Maybe the film is a statement about homosexuality. The Interzone society gives a new meaning to the term "boy's club."
Or perhaps, it's some combination of the above. In the end, Naked Lunch creates a disturbing, bleak, and depressing world for its protagonist. While it lacks coherence, it's definitely worth checking out for the visceral imagery.