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.
Charlie goes home and waits for Fay to return from dancing. When she arrives, he is sexually aggressive. They make love, and he senses the “other” Charlie watching them but not panicking. Charlie and Fay begin an affair, and he soon loses the sense of the other Charlie’s surveillance. Charlie decides to go back to the lab and take over research on the experiment. One day Algernon attacks Minnie and bites Fay. Charlie is concerned by Algernon’s hostility.
The Welberg Foundation, which is paying for the experiment, agrees to allow Charlie to work at Beekman without having to report to Nemur. Charlie returns to the lab, and Burt begins working with Algernon again. He is disturbed to discover that Algernon’s problem-solving abilities seem to have regressed. Charlie asks Nemur what contingency plans have been made for him if his own intelligence should not hold. Nemur tells him that should he become retarded again, he will be sent to the Warren State Home. Charlie decides that he needs to visit Warren to see what may await him.
Charlie’s anticlimactic visit with his father brings into focus his notion that there are two Charlie Gordons, the former mentally disabled simpleton and the current genius. This idea has been implicit in Charlie’s dreams and hallucinations but only now becomes apparent and real to him. Though Matt has never been strong enough to fully defend Charlie against Rose’s tyranny, he has always supported his son, and for that reason Charlie feels warmly toward his father. Charlie is unable to bring himself to reveal his identity to Matt because he knows that he is no longer the Charlie Matt once knew. Just as the bakery workers are not proud of Charlie’s new intellect, Charlie fears that Matt will have no reason to feel anything but threatened by his genius son.
Charlie’s relationship with Fay represents a step forward in his personal and emotional development. Fay is the first significant character in the novel who does not know that Charlie used to be mentally disabled. Though Charlie has mentioned brief interactions with professors at Beekman who do not know about his past, Fay is the first new acquaintance with whom he allows himself to have a personal relationship. Fay is unlike anyone else in his world: when she talks about her loathing of straight lines, it implies that she is entirely uninterested in the world of science and intellectual pursuits. Fay’s odd way of being is purely emotional, and she is thus an appropriate teacher for the emotionally crippled Charlie.
Though Charlie realizes in this section that emotional troubles cannot be solved in the same manner as intellectual puzzles, he nonetheless maintains a scientific approach to his emotional development. He observes his own behavior in a number of sexually tense situations in an attempt to determine what is causing his confusion. Much as Burt might conduct an experiment by building different mazes for Algernon, Charlie constructs different sexually charged situations to see how the other Charlie will react. While the other Charlie objects violently to the prospect of intimacy with Alice, he is merely curious about intimacy with Fay. This difference may arise from the fact that the old Charlie does not know Fay and does not have the residual feelings of overwhelming love for her that he has for Alice. Charlie’s attempt to make love to Alice while pretending she is Fay is, in effect, an experiment to see if the other Charlie can be tricked into calmness. However, Charlie is unable to go through with his experiment because he realizes that doing so would be tantamount to treating Alice as an inhuman, scientific factor, just as Nemur had callously treated him.
Keyes strengthens the parallel between Charlie and Algernon by introducing Minnie, a female companion for Algernon, around the same time that Charlie begins his affair with Fay. However, Algernon’s increasingly erratic behavior is a frightening omen of what lies ahead for Charlie. Algernon’s attack on Minnie creates suspense by leading us to wonder if Charlie will soon lash out at Fay, or even at Alice. When we learn that Algernon’s intelligence has already begun to desert him, we know that Charlie’s decline cannot be far off. The other Charlie, the Charlie from the beginning of the novel, is waiting in the wings to reassert himself.
Charlie's "friends" laughed at him because he was cognitively impaired, and in the beginning, he wasn't really sure why so he just laughed along with them.