Naked Lunch is a non-linear narrative without a clear plot. The following is a summary of some of the events in the book that could be considered the most relevant.
The book begins with the adventures of William Lee (also known as "Lee the Agent"), who is Burroughs' alter ego in the novel. His journey starts in the US where he is fleeing the police, in search of his next fix. There are short chapters here describing the different characters he travels with and meets along the way.
Eventually he gets to Mexico where he is assigned to Dr. Benway; for what, he is not told. Benway appears and he tells about his previous doings in Annexia as a "Total Demoralizator". The story then moves to a state called Freeland — a form of limbo — where we learn of Islam Inc. Here, some new characters are introduced, such as Clem, Carl, and Joselito.
A short section then jumps in space and time to a marketplace. The Black Meat is sold here and compared to "junk", i.e. heroin. The action then moves back to the hospital where Benway is fully revealed as a cruel, manipulative sadist.
Time and space again shifts the narrative to a location known as Interzone. Hassan, one of the notable characters of the book and "a notorious liquefactionist", is throwing a violent orgy. AJ crashes the party and wreaks havoc, decapitating people and imitating a pirate. Hassan is enraged and tells AJ never to return, calling him a "factualist bitch" - a term which is enlarged much later when the apparently "clashing" political factions within Interzone are described. These include the Liquefactionists, the Senders, the Factualists, and the Divisionists (who occupy "a midway position"). A short descriptive section tells us of Interzone University, where a professor and his students are ridiculed; the book moves on to an orgy that AJ himself throws.
The book then shifts back to the market place and a description of the totalitarian government of Annexia. Characters including the County Clerk, Benway, Dr Berger, Clem and Jody are sketched through heavy dialogue and their own sub-stories.
After the description of the four parties of Interzone, we are then told more stories about AJ. After briefly describing Interzone, the novel breaks down into sub-stories and heavily cut-up influenced passages.
In a sudden return to what seems to be Lee's reality, two police officers, Hauser and O'Brien, catch up with Lee, who kills both of them. Lee then goes out to a street phone booth and calls the Narcotics Squad, saying he wants to speak to O'Brien. A Lieutenant Gonzales on the other end of the line claims there's no one in their records called O'Brien. When Lee asks for Hauser instead, the reply is identical; Lee hangs up, and goes on the run once again. The book then becomes increasingly disjointed and impressionistic, and finally simply stops.