Charlie is a 32-year-old man with an I.Q. of 68, who has struggled his whole life toward the goal of "being smart." This goal is actually his mother's obsession, and when she realizes the futility of it, she threatens to kill him. Charlie's father takes him to his Uncle Herman's to live. There he lives until the age of seventeen, when Uncle Herman dies. Mr. Donner, a good friend of Uncle Herman's, promises to take care of Charlie the rest of his life. Mr. Donner is a bakery owner, and he guarantees that Charlie will always have a place to sleep, a job, and food to eat.
Charlie wants to be smart and enrolls in classes at the Beekman Center for Retarded Adults, where he learns to read and write. He also meets Miss Kinnian, who recommends Charlie to the team of doctors from the psychology department at Beekman University for experimental surgery. This neurosurgery stimulates Charlie's brain centers and increases his ability to learn, thereby increasing his intelligence.
Over a nine-month period, Charlie keeps "progress reports" documenting his transformation. Charlie's I.Q. eventually in-creases three-fold, bringing many revelations with it.
Charlie is able to reconstruct his life from many recovered memories, and he experiences many new things. His relationship with Miss Kinnian goes full circle. Initially their relationship is one of teacher/student, then platonic friends, then lovers, and finally returns to teacher/student. Throughout the many changes in Charlie's life, one element stays constant: the value that he places upon friendship. The experiment's outcome was never certain; ironically it is Charlie, with his increased intelligence, who is able to predict its outcome. His mental regression is quick and painful to himself and everyone who knows him. He perhaps regresses to less than his original state but seems to retain occasional flashes of what his evolved life had been. At the end of the novel, Charlie chooses to move to the Warren State Home, believing that doing so will be easier for his friends.