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Charlie Gordon: 32 year old mentally retarded man; works at Donner's Bakery as a janitor
Alice Kinnian: Charlie's teacher at the Beekman College Center for Retarded Adults; becomes a love interest for Charlie
Professor Nemur: the scientist in charge of the experiment that increases Charlie's intelligence
Dr. Strauss: the neurologist and psychiatrist whom performs the experimental operation on Charlie
Burt Selden: a graduate student working on his PhD and who oversees Charlie and Algernon's tests
Algernon: the mouse who is the first successful test subject for the experimental operation that Charlie also undergoes
Fay Lillman: Charlie's neighbor; an artist, free-spirited and loves to dance; has an affair with Charlie
Rose Gordon: Charlie's mother; refuses to accept Charlie's retardation
Matt Gordon: Charlie's father; sells barbershop supplies
Norma Gordon: Charlie's younger sister; takes care of Rose when she grows up
Uncle Herman: Charlie's uncle who takes him in when Rose kicks him out of the house; also sets a job up for Charlie and Donner's bakery.
Mr. Donner: the owner of the bakery at which Charlie works; a friend of Uncle Herman
Frank Reilly: a co-worker at the bakery who picks on Charlie
Joe Carp:
a co-worker at the bakery who picks on Charlie
Gimpy: the head baker who has a limp; protects Charlie a little more than Frank and Joe
Fanny Birden: works at the bakery and is consistantly nice to Charlie
Dr. Guarino: the quack doctor Rose takes Charlie to to increase his intelligence
Hilda: Charlie's first nurse after his surgery; believes Charlie is defying god by unnatural intelligence
Minnie: the mouse Fay buys to accompany Algernon
Meyer Kalus: a new employee of Donner's bakery who is there when Charlie resumes working
The story is told from Charlie Gordon's progress reports, which Dr. Strauss and Professor Nemur have asked him to write. Charlie goes to Beekman College Center for Retarded Adults to learn how to read and write. At the same college, Charlie participates in several tests. He does not understand the Rorschach tests Burt administers because he does not understand the concept of seeing images in the ink blots. He also does not remember how he learned about the Beekman School. A woman gives the thematic apperception test, but does not want to make up lies about the people in the picture. The scientists also have Charlie race Algernon, and he gets a shock if he goes the wrong way in the maze. Charlie always loses to Algernon, which frustrates him. Dr. Strauss and Nemur find Norma, Charlie's sister, who lives with their mother and she gives them permission to do the surgery. Nemur is worried that Charlie will get sick from the change from low to very high IQ., but Burt and Strauss are confident that Charlie is the best person for the experiment. Ms. Kinnian tells Charlie that Dr. Strauss and Professor Nemur have chosen him for their experiment. They also warn him that it might not work and that he could end up worse than he already is. Before his surgery, Burt brings him flowers and Joe Carp brings him a cake.
After his operation, Hilda, the nurse, vocalizes her belief that the doctors do not have a right to mess with what God has done. Hilda is replaced by Lucille. Mr. Donner says that Charlie will always have a position at the bakery for life, just like he promised Charlie's Uncle Herman. Charlie remembers that he learned about the Beekman College from Fanny Birden, a worker at the bakery. Dr. Strauss brings Charlie the night TV to listen to when he is sleeping. Charlie does not understand how it will work and loses sleep from keeping the volume up too loud. Charlie goes to the bar with Frank and Joe and they make him go around the corner to see if it is raining and they ditch him. Charlie waits a long time, but he gets lost and a nice cop brings him home.
Shortly after the operation, Charlie beats Algernon when they race, and now he wants to be Algernon's friend. Charlie starts his education with Ms. Kinnian. First, he reads Robinson Crusoe and feels bad that the main character is all alone. He asks why he has to be all alone. Charlie is a delivery boy and janitor at the bakery. By watching the workers, he learns how to use the mixer, which surprises a lot of people. Ms. Kinnian teaches him the rules of punctuation. Charlie begins to have memories of his childhood. He remembers his mother hitting him when he held his baby sister. Back to the present time, Charlie goes to a party with his "friends" from the bakery and he realizes that they have been playing tricks on him this whole time. When he goes home, he remembers dancing with Ellen and has a wet dream.
Since the surgery, Charlie has developed a photographic memory, allowing him to read books very quickly while retaining the information. He remembers how the older kids used to pick on him at school. Dr. Strauss thinks he's still a boy when it comes to women, meaning emotionally and sexually he is at an adolescent state. He starts doing free association with his memories during his sessions with Dr. Strauss and in his journal. When he was 11 he wanted to give Harriet, the prettiest girl in the school, a valentine. He gives her his locket and has his "friend" Hymie right a letter. Charlie is unaware that Hymie wrote Harriet an inappropriate letter, and her older brothers beat Charlie up for what he wrote to her. He does the Rorschach tests again and he becomes angry and suspicious that Burt was making fun of him when he first tried to do the test.
Gimpy and Frank teach him how to makes rolls at the bakery, but he forgets when they tell him to do it alone. Nemur wants to present their paper in 6 weeks and he is not afraid of regression anymore because Algernon is still maintaining his intelligence. Charlie remembers that his mother's name is Rose and his father's is Matt. He knows their voices but their faces are blurred when he tries to remember them. He remembers that the teacher and principal want him to leave PS 13 and go to PS 222, a special school. Rose won't stand for it and is determined to make Charlie normal.
He goes to dinner and a movie with Ms. Kinnian and ends up frustrated with her and himself. Back at the bakery, he catches Gimpy stealing and does not know what to think about it. He talks to Ms. Kinnian and she tells him that he needs to trust himself to make the right decision about Gimpy. At this point he knows he is in love with Ms. Kinnian. Charlie decides to tell Gimpy to stop stealing or he will tell Donner, and Gimpy says that he will stop stealing. Charlie and Ms. Kinnian go to a concert and Charlie sees a boy watching them, but decides it was a hallucination. He later realizes that the boy was the old Charlie, and that he is still an adolescent emotionally when it comes to sex.
He is going to lose his job at the bakery because everyone is afraid of him and feels inferior. Everyone but Fanny signs the petition and Mr. Donner cannot ignore their plea. Charlie remembers that his mother used to beat him when he would get an erection. As his intelligence increases his love for Alice decreases because they cannot communicate anymore. He meets a woman in Central Park and she asks him to sleep with her. She shows him that she is pregnant and he freaks out because he thought of his mother being pregnant with Norma. He cannot think about sex if it includes his mother or Norma.
Charlie starts recording himself on a tape rather than type his journals. He has the fear of being strapped in. He remembers going to see Dr. Guarino, who might be able to make him normal again. The doctor straps him down and the machine is loud, which upsets Charlie until he pees his pants. His mother always hit him when he peed in his pants. His parents argue about money and how Rose has wasted it on phony doctors. Charlie realizes that he wants to be smart because his mother wanted him to be smart. After Norma was born, Rose stopped caring as much about Charlie because she was able to have a normal child. He liked Dr. Guarino because he was nice to him and treated him like a human being, not like how Nemur treats him. While at the conference in Chicago, Nemur describes the process of the operation. Charlie mentions Rahajamati and Tanida's works, but neither Nemur nor Strauss have read them because they are recent and in Hindi and Japanese. Burt says that Nemur's wife pushes him and stresses him out too much. During the session, Burt explains that at the peak of Algernon's intelligence he would not do the lock problem no matter how hungry he was, or he would solve the problem but not eat. Charlie wonders why Burt had never told him about Algernon's recent behavior. They show pictures and videos of Charlie before and after the operation to show his change. Nemur admits they had made a mistake, and that the waiting period had not been long enough to see if the change would stick. Charlie lets Algernon out of his cage while Strauss is speaking and he runs into the bathroom. While everyone is looking for him, Charlie pockets him and takes him back to New York.
Charlie buys his own apartment so he can get away from Beekman and the scientists. He locks himself out of his apartment and goes next door to use the fire escape. He meets Fay, his neighbor, who is a sexually free artist. Charlie finds out that Matt has his own barber shop now and goes there. He does not tell Matt that he is his son despite his plan. Rose threatened to kill Charlie if Matt did not take him away. Matt took him to stay with Uncle Herman. Charlie makes a 3-D maze for Algernon, but he notices his erratic behavior. Fay comes over and gets him drunk. As they are about to have sex, he begins to act like the old Charlie. Fay buys Algernon a female mouse to keep him company, and name her Minnie.
Charlie goes to a local diner and the bus boy drops and breaks several dishes. People in the restaurant laugh at him because he is mentally retarded. Charlie's turning point occurs when he finds himself laughing at the boy too. He decides to start working on a project that will better science intelligence. Charlie discovers that it was not his intellectual barrier but that the old Charlie was keeping him away from women. For some reason, the old Charlie won't let him make love to Alice. He wants to see what will happen if he has sex with Fay, so he gets drunk and waits for her to come home. He then lets the old Charlie watch as he makes love to her. Minnie is becoming afraid of Algernon and his erratic behavior. Algernon bites Fay and also badly attacks Minnie, but is still alive. Algernon has a sense of urgency in his behavior. Charlie starts working at the lab and learns that Nemur and Struass plan to put him in the Warren home should he regress worse than before.
Charlie goes to visit Warren to see what its like. There is not much hope there but there are a lot of people who give themselves to help. Algernon has a decrease in motivation. Alice and Fay meet when Alice comes to see Charlie, and they get along well. The only thing Alice does not like about Fay is that she gets him drinking, which distracts him from his work. Algernon lies in his own waste and does not do anything for long periods of time. Fay gets a new boyfriend who has time for her. At this point, Charlie is at his peak intelligence. He goes to a party Mrs. Nemur is throwing and gets into an argument with Nemur. Strauss explains his recent disassociation with the old Charlie. Charlie's hypothesis is that intelligence without the ability to give and receive affection leads to mental and moral breakdown, to neurosis, and possibly even psychosis. Charlie gets drunk and the old Charlie comes out in the bathroom mirror. He tells him that he is not going to give up the intelligence without a fight. He agrees with Nemur now that he has become selfish and ignorant. Charlie was about to fall asleep when the answer to the problem came to him. The Algernon-Gordon Effect, which says that artificially induced intelligence deteriorates at a rate of time direction proportional to the quantity of the increase.
He becomes absent minded and has headaches. Algernon dies and dissection proves Charlie's hypothesis is correct. He buries him in the backyard and puts flowers on his grave. He decides to go see his mother, but Rose does not remember much these days and she went in and out of a trance. Rose is proud that her boy went to college and became a professional and he gives her a copy of his scientific work to show people. Norma was very happy to see him and wants him to stay, but he cannot get up the nerve to tell her his intelligence is only temporary. Rose snaps when they hug and threatens him with the knife like she did 20 years ago. Norma understands why they made him leave now: Rose accused him of having sexual thoughts for his sister.
Charlie has become edgy and irritable. He is hostile towards Strauss in a session, and he hallucinates. He decides not to have any more sessions, and he does not want to see them anymore. He does the maze puzzle slower and he tries the Rorschach again, but cannot remember what he needs to say in order to be 'normal'. He keeps changing his answers and becomes frustrated until he decides not to do any more tests at all. He does not remember books he read a few months ago and a policeman has to take him home because he does not remember where he lives. Alice comes to check on him and they have sex because Charlie is able to realize that she was not Rose or Norma and that it is alright. She promises that she will leave when he tells her to and she wont follow him to Warren. Charlie is at her level again, but his memory worsens, demonstrating signs of senility. Last things he learned are the first forgotten. He becomes easily irritable with Alice, and his motor activity is impaired. He notices that Alice is pitying and humoring him. He is always looking at life through a window, and the child in him is reclaiming his mind. Charlie has lost all his foreign languages and does not understand the paper he wrote a few weeks earlier. He has also lost his smile and respectfulness. Charlie makes Alice leave because she is too much like his mother and does not want her pitying him.
Charlie thinks that if he starts learning new things that he will stand still rather than go all the way back in a regression. The landlady Mrs. Mooney checks in on him and brings him food periodically paid for by Alice. Writing takes longer and Charlie has to look up words in the dictionary when he forgets how to spell them. He loses his check and lucky rabbits foot. He needs to get a job to pay the rent so Alice wont pay it for him. He goes back to the bakery and explains what happened to Mr. Donner and he gives him his job back. Meyer Klaus had taken Charlie's position while he was gone, and he picks on Charlie to the point where he cries and pees his pants. Joe defends him and Frank and Gimpy want to get him fired, but Charlie says that it is ok because Klaus apologized. He has his friends back and he is happy. Then, he accidently goes to adult school and Ms. Kinnian leaves crying. He realizes that he is the cause of her sadness and decides to go the Warren home. Now Charlie sees the smart Charlie in the window. In his last entry, he asks someone to put flowers on Algernon's grave.
