I wasn’t his son. That was another Charlie. Intelligence and knowledge had changed me, and he would resent me. . . .
Charlie sees a newspaper article that contains an interview with Norma, in which Norma insists she does not know Charlie’s whereabouts. Charlie learns that his mother told Norma that he had been sent off to the Warren State Home, an institution for the mentally disabled, and had died there years ago. Charlie also reads that his father now owns his own barbershop and no longer lives with his mother. Charlie recalls that after Norma’s birth, Rose had stopped longing for him to become normal and had started wanting him to disappear.
Charlie moves into an apartment in the city. He builds Algernon an elaborate maze to solve and meets his neighbor Fay Lillman, a free-spirited and flirtatious artist. Fay is appalled by the neatness of Charlie’s apartment, saying she cannot stand straight lines and that she drinks to make the lines go blurry. Charlie finds Fay strange but undeniably attractive.
Charlie visits his father at his barbershop. Matt does not recognize his son, and treats him as a customer. Too nervous to say anything, Charlie gets a haircut. He remembers the night that his father took him to live with his Uncle Herman after Rose had become hysterical, threatening that she would kill Charlie with a carving knife if he were not shipped out to the Warren State Home immediately. Charlie attempts to reveal his identity to Matt, but after an awkward and inconclusive exchange, he gives up and leaves the shop.
Algernon performs well in Charlie’s new mazes but sometimes appears to be angry or depressed, frenetically throwing himself against the walls. Fay buys Algernon a female companion mouse named Minnie. Fay stays in Charlie’s apartment one night. They have drinks together and Charlie passes out. The next morning, naked in bed together, Fay says that they have not made love and wonders whether Charlie is gay. She tells him that he acted like a little kid while he was drunk. Charlie realizes that the old, mentally retarded Charlie has not left him and that his former self still exists within his mind.
Charlie spends a day in movie theaters and wandering the streets, just to be among other people. He eats at the diner where he took Alice after their movie date. A mentally disabled busboy accidentally breaks some dishes, and as he sweeps up the mess, the customers taunt him cruelly. Not comprehending that he is the target of the customers’ mockery, the busboy smiles along with their insults. Charlie is infuriated and screams to the crowd that the busboy is human and deserves respect.
Charlie visits Alice and talks over his feelings with her. He worries that he has become emotionally detached from everyone around him, and he yearns to reconnect with humanity. Charlie wonders if the inner, mentally retarded Charlie would allow him to make love to Alice if he pretended that she were Fay. He hypothesizes that since he cares for Fay less deeply than he does for Alice, his inner self might not panic at the notion of sex with Fay. Charlie turns out the lights and begins kissing Alice but is unable to trick himself into believing that she is Fay, and he feels guilty for trying to use her in an emotional experiment.