Charlie sees a newspaper picture of his mother and sister, who were questioned by a reporter following Charlie’s escape with Algernon from the convention. From the article, Charlie learns the address of his mother, as well as the fact that his father and mother have separated and his father owns a barbershop in the Bronx. The sight of his mother’s face reminds him of the final showdown between his parents: his mother wanted Charlie to be placed in the Warren home, but his father instead takes him to his brother Herman’s.

Charlie finds an apartment in midtown New York City. He continues his studies and builds a new maze for Algernon. Across the hall is a free-spirited painter named Fay. Sexually attracted to her, Charlie keeps his distance, fearing the re-emergence of the shadow Charlie.

Deciding to visit his father, Charlie shows up at the barbershop. His father does not recognize him, so Charlie asks for a shave and haircut. He asks his father if he knows who he is. Matt Gordon is fearful, so Charlie leaves without revealing his identity.

Fay brings Algernon a female mouse for companionship. When she later comes to Charlie's apartment following an altercation with another man, she almost succeeds in convincing Charlie to go to bed with her. Charlie gets drunk, and during his drunken episode he reverts to the old Charlie, which startles Fay. Charlie goes on an “anti-intellectual binge,” going to the movies and afterward to a bar. One of the busboys is mentally handicapped. The other customers are making fun of him, and Charlie is laughing along when he realizes what he is doing. He shouts out for everyone to leave the boy alone—he is a human being.

The next day he calls Alice Kinnian and tells her that he will return to the lab after he has finished a few projects of his own. He goes to visit her and comes close to making love to her, but the shadow Charlie shows up and prevents it once again. He goes back to his apartment, visits Fay, and eventually manages to make love to her, no longer caring if the shadow Charlie watches.

One day in July, Algernon bites Fay. He also attacks Charlie, who sees that the female mouse that Fay brought has been bitten and gashed by Algernon. It is clear that Algernon is becoming aggressive and antisocial. Charlie knows he has to get the mouse back to the lab to determine if what is happening to Algernon is happening to himself.