In the days following the operation, Charlie becomes increasingly frustrated. He thinks the puzzles, the games, and especially the progress reports are “stupid.” He gets headaches from trying to remember as Dr. Strauss and Professor Nemur want him to. Miss Kinnian assures him that he will get smarter, but it will happen without his realizing it.
Charlie eats lunch with Burt in the college cafeteria. He listens to the students around them and hopes that he will soon be able to have similar conversations about serious topics. Burt promises him that eventually he will be smarter than the students. Charlie almost tells the students that he will be very smart like them, but Burt interrupts him, as the experiment is still secret. He explains that Professor Nemur does not want his colleagues to laugh at his theories of intellectual enhancement.
Almost two weeks after the operation, Charlie is given permission to go back to the bakery. When he shows up for work, the other men poke fun of his bandages, asking if he had "brains put in." Charlie discovers that Mr. Donner has hired a boy to take over the deliveries that Charlie used to make. When Charlie is concerned that he will lose his job, Mr. Donner explains that he had promised Charlie’s uncle that he would take care of Charlie and give him a job for the rest of his life. Charlie is relieved and enjoys the joking around of the other men, though it is actually mean-spirited name-calling directed at Charlie. Whenever someone makes a mistake, they call it making a “Charlie Gordon.”
At night, Charlie is connected to a subliminal teaching machine. Dr. Strauss explains that it will help Charlie get smarter even as he sleeps. Charlie, however, is upset that he cannot sleep because of the noise. Eventually Dr. Strauss lowers the volume. The machine is also intended to help Charlie’s long-term memory. Charlie eventually remembers how he came to Beekman University to learn with Miss Kinnian. A coworker at the bakery had a cousin who was a student there. Through this connection, Charlie was registered as a student too.
At a work party, the other men make fun of Charlie and trick him into getting drunk. They leave him alone on the streets. Charlie is lost and frightened until a policeman takes him home. Charlie vows never to drink whiskey again.
On March 29, twenty days after the operation, Charlie finally beats Algernon at the maze. Charlie recognizes the significance of this in terms of his operation, but he confesses that he does not feel any smarter. Charlie is also remembering his past in his dreams, recalling incidents of being punished and his sister making fun of him.
Miss Kinnian begins to give Charlie private lessons. She has him read Robinson Crusoe. Charlie confesses there are many words he does not know, but he has a basic understanding of the story. His spelling begins to improve as he continues writing progress reports.