The final progress report opens with Charlie realizing that his mind is changing. He's very irritable and often fights with his neighbors. He hates to sleep because of nightmares and the fact that he resents wasting any time. He has contemplated suicide, but he feels that such an act wouldn't be fair to the old Charlie.
Charlie has a strange therapy session with Dr. Strauss, during which he has an odd sense of disassociation, perhaps a hallucination or a spiritual awakening. Charlie feels that he is moving outside of his body, expanding outward and upward, like a bubble, into a universal consciousness. He becomes completely disassociated from his body. But the experience doesn't last, and he is drawn back into his body. Charlie awakens to Dr. Strauss shaking him. Charlie insists that he doesn't want to have any more sessions with Strauss, that he has seen enough.
Charlie is no longer dictating his reports. He returns to the lab and doesn't perform well on the maze test. He becomes angry and tears up the test. He argues with Burt Selden but then realizes that it's not Burt's fault. Charlie becomes frustrated over the Rorschach test. He rifles through the inkblot cards, knowing that he is supposed to respond in a particular way but realizing that he can no longer respond as he should. He becomes angry and informs Burt that he won't be returning to the lab anymore.
Strauss attempts to visit Charlie, but Charlie won't let him in. Charlie laments how books he recently read no longer make sense to him. He has a vision of himself at an early age; his mother is trying to teach him to read, but he's not performing very well. He asks God not to take all of his intelligence away.
Charlie comments that he normally takes a walk at night, but the previous night he got lost and a policeman helped him home. He senses that this has all happened to him before.
Charlie returns one evening and finds Alice in his apartment. Fay has informed her that she has been worried about him. Alice has cleaned up Charlie's apartment. This angers Charlie, and he says that he doesn't want to see anyone because he doesn't want anyone to feel sorry for him. Alice tells him that she wants to spend whatever time is left with him. When he kisses him, he doesn't experience any panic and they make love. For Charlie it's another spiritually uplifting moment, similar to the experience he had in therapy with Dr. Strauss. He deeply understands the powerful need for human connection. Charlie accepts Alice, and she agrees that she will leave when he tells her it's time to go. Charlie takes comfort in Alice's company, and her presence makes him want to fight the regression.
Charlie is angry at his inability to remember. He seems to come in and out of awareness. He wonders if it's possible to fight the regression, and he imagines the old Charlie staring at him from behind a window. His memory is getting worse, and he's becoming confused. He tries to reread his report, but it no longer makes sense to him. It feels as if someone else has written it.
Charlie begins having trouble with his coordination. He watches a lot of television, continuing to watch even the test pattern when the station signs off. The pattern reminds him of a window, and he asks why he is "always looking at life through a window." He feels that the childish old Charlie is starting to reclaim his mind. Whereas before it was important for him to learn about his past, now he wants to forget the details of his former life. He tries to read an article in German that he had used in his research, but he is no longer able to read the foreign language.
Alice and Charlie argue about their living conditions, saying that he was a more humane individual as the old Charlie than in his current state. She tells him that he has lost something important that the old Charlie possessed: a certain innocence. Charlie tells himself that he has been having more and more trouble following Alice's conversations. He tells her that it's time for her to leave, but she says that she doesn't want to go yet. He upsets her by saying that her presence is hurting him rather than helping. He comments that although she's trying to keep his mind active, to make him think, it's bound to fail. He deliberately tells her that he no longer wants her help. As a result, she leaves.
Charlie's coordination worsens. He can no longer use the typewriter. However, his depression lifts as he considers that perhaps Alice was right. He can't stop the loss of old knowledge, but perhaps if he keeps learning new things he can halt the downward spiral. He thinks that reading is the key. As long as he keeps reading, he should keep learning new things. Strauss visits him, but Charlie resents the visit. He tells Strauss not to worry, that when his mind regresses too much he'll take himself to the Warren Home. Charlie tries to talk to Fay, but she seems afraid of him now. His landlady drops by to bring him some soup; Charlie feels she's probably been put up to it by Alice and Strauss.
Charlie doesn't make a journal entry for a week and can't understand how time has gone by so quickly. His writing is starting to exhibit mistakes in punctuation and sentence structure. He thinks he has spent much of the week in bed, staring out the window. He's still trying to read, but many of his books are now too difficult for him to understand. He comments on reading a book about a man who thought he was a knight, not recognizing the book is Don Quixote. He becomes angry because he thinks he used to understand such things. The act of writing is becoming increasingly harder for him; he even has to look up simple words in the dictionary.
Charlie recounts how each night he looks out his window and watches a woman in another building, as she takes a bath. It excites him, but at the same time makes him feel lonely. He understands that this isn't a nice thing to do, but he can't help himself.
Charlie writes that his landlady is worried about him. She asks if he is sick or simply a "loafer," noting that she doesn't like loafers. Charlie tells her that he thinks he's sick. Reading and writing are becoming increasingly difficult, and he's always tired. He decides that he will make his reports easier to write by using only simple words. He comments that it is getting colder outside, but he still goes to put flowers on Algernon's grave. His landlady tells him it's silly to do this, but Charlie insists that Algernon was a special mouse. Charlie visits Fay, but she turns him away. He comments, without reflection, that she has a new lock on her door.
Charlie's world is now restricted to his apartment. He complains that it is cold. His television is broken, and he keeps forgetting to get it fixed. His spelling is now incorrect, and the woman he has been watching now pulls down her shade.
The landlady brings a doctor to see Charlie, and Charlie becomes angry when he feels the doctor is making fun of him. Charlie tells the doctor that he used to be a genius, and the doctor laughs. When the doctor asks if he has any friends or relatives, Charlie replies that he used to have a friend named Algernon. He thinks he has been having bad luck because he has lost his rabbit's foot and horseshoe.
Strauss and Alice visit, but Charlie doesn't let them in. The landlady tells Charlie that they left money for his food and rent, but he doesn't want to take charity. The landlady suggests that he get a job. Charlie remembers the bakery but doesn't want to return there because the people will probably make fun of him. He again contemplates returning to the Warren Home.
Eventually, Charlie can no longer read his old progress reports; he can only read picture magazines he purchases at the drugstore. He has strange dreams about the women in the magazines and feels that his dreams are inappropriate.
Alice visits again, but Charlie refuses to let her in. Even though she cries, he's afraid that she will laugh at him. Charlie remarks that he still loves her and that he needs to get a job.
Charlie returns to the bakery. He notes that Mr. Donner is very nice but suspicious of him. He explains his condition to Donner and returns to his old job as janitor. He tells himself not to be upset if the others laugh at him because they aren't really as smart as he once thought they were, and they were once his friends. A newer employee mistreats Charlie, making him so afraid that he wets himself. Joe, Fred, and Gimpy stick up for Charlie and threaten to have the new man fired. Charlie tells them the man shouldn't be fired because he has a family and because he apologized for his actions and Charlie was sure it wouldn't happen again. Gimpy tells Charlie that he has friends at the bakery and that Charlie should come see him if anyone ever mistreats him again.
Charlie returns to Alice Kinnian's class, forgetting that he is no longer enrolled in it. He returns to his old seat and tells Alice that he has lost the book he was reading. Alice cries and leaves the room, and Charlie has a flash of memory about the operation and his former intelligence. He notes that he "reely pulled a Charlie Gordon." He doesn't recognize the other students in the class, and he leaves before Alice returns. He decides to go to the Warren Home because he doesn't want anyone feeling sorry for him. He wants to go to a place where no one knows Charlie Gordon and where there are others like himself. He notes that he has a new rabbit's foot and lucky penny.
In the report he tells Alice not to feel sorry for him, that he appreciated having been able to understand the world and reconnecting with his family, if only for a short time. He's not sure why he's dumb again or what he did wrong. He has a vision of seeing another man through a window, a man who looks much like himself but talks and acts differently. Charlie has now forgotten everything about his contribution to science.
In the final lines of his journal Charlie says goodbye to Miss Kinnian, Dr. Strauss, and everyone else and asks that they put some flowers on Algernon's grave.
From the opening lines of this report, it is very clear that Charlie's mental regression is happening quite rapidly. He loses his higher-order abilities: he can no longer think critically or read and write effectively. When Charlie fails to recognize or understand Don Quixote, we realize that he can no longer comprehend deeper meaning, like symbol and metaphor. The brevity of his journal entries indicates that the act of writing is becoming increasingly harder for him and that his thoughts are becoming less sophisticated.
He also begins to withdraw emotionally. Though he initially accepts help from Alice, it is as if his world were shrinking. Through his refusals to get help and his deliberate insult of Alice we see his desire to retain a certain amount of dignity, and in his decline we see one of the indomitable human traits: the desire to fight for one's possessions. Instead of become depressed and simply giving in to the regression, Charlie ties to fight it off. When that doesn't work, he attempts to at least keep it in check.
Charlie's ability to make love to Alice without experiencing any panic suggests that he has finally exorcised the demons of his subconscious. As they make love, Charlie understands the deep need for human contact and realizes that he truly loves Alice.
As the regression reaches its final stage, we see the old Charlie being to take over. Charlie's writing become markedly less sophisticated, and his understanding of the events around him becomes less clear. His former grasp of the world is gone.
The bakery workers' new attitude toward Charlie, one of compassion and protection, suggests that it is possible for people to change, to have more compassion for others. This notion lends an uplifting quality to the novel.
The final lines of the novel reveal that the old Charlie has completely replaced the new Charlie, who has receded somewhere into the depths of Charlie's mind.