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Charlie Gordon: 37 year old man with learning disabilities and an I.Q. of 68. He works at the plastic box factory
Alice Kinnian: 34 year old teacher at a night school for adults with learning disabilities
Mrs. Flynn: Charlie's landlady
Dr. Strauss: 50 year old neurosugeon
Dr. Nemur: 60 year old
pyschologist
Burt: Graduate student working for Nemur and Strauss to get his PhD. He also does all the testing on Charlie
Mr. Donnegan: friend of Charlie's uncle and the man who runs the factory
Frank Reilly: one of Charlie's 'friends' that works at the factory
Joe Carp:
one of Charlie's 'friends' that works at the factory
Fanny Birden: works with Charlie at the factory and is the only one who does not sign the petition
Algernon: the mouse who underwent the same surgery as Charlie to raise his intelligence.
The story is told from Charlie's progress reports. Charlie goes into the hospital to do some tests. He fails the Rorshach tests because he does not understand the concept of seeing images in the ink blots. He also can not do the Thematic Apperception test, which involves making up a story about a picture. The scientists also have him race Algernon, a mouse that has underwent an operation to triple his intelligence, in different maze tests, in which Charlie always loses. Ms. Kinnian tells Charlie that Dr. Strauss and Dr. Nemur have chosen him for their experiment, but they warn him that it might not be permanent. They chose Charlie because he is well tempered and has a high level of motivation to learn how to read and write. After the operation, several days pass before the scientists see any results. Because of this, Charlie gets very upset that he still cannot beat Algernon. At the factory, Frank Reilly and Joe Carp make fun of Charlie, but he does not realize it. After Charlie skips an appointment at the hospital, Dr. Strauss brings him a television-like machine to play when he sleeps. Charlie does not understand how he is supposed to learn anything while he is sleeping. Frank and Joe take Charlie to a bar, and then trick him so they can ditch him.
Shortly after, Charlie is able to beat Algernon in the maze races. He immediately begins his new education by reading Robinson Crusoe. Charlie also begins to question authority and ideas. He also learns about punctuation from Ms. Kinnian. Charlie goes out with Frank and Joe again only to realize that they have been making fun of his all this time, which he takes very hard. He now thinks that everyone is making fun of him, even Burt who administers his Rorshach tests. Once people at the factory realize that Charlie is getting smarter, they start avoiding him. Charlie overhears the doctors arguing, and realizes that Dr. Nemur only wants to get published and the Dr. Strauss is ridding on Nemur's experiment. Charlie also becomes aware of how young and beautiful Ms. Kinnian is, and falls in love with her. At the same time, Alice Kinnian begins regretting putting Charlie through the experiment, despite the fact that Algernon is still very intelligent.
Workers at Donnegan's Factory make a petition to make Charlie leave the factory, and he quits. Fanny is the only worker that did not sign it but she thinks Charlie is going against God by changing his intelligence. Later, Charlie and Algernon are presented to the American Psychological Association. Charlie mentions other researchers' finds on Nemur and Strauss's experiment, but neither of them know how to read Hindi or Japanese. This is when Charlie realizes that his creators are not geniuses at all, but instead they have been taught by narrow specialization. Charlie starts to believe that people have been hiding their true selves from him. He also starts to become less sociable because he can no longer relate to anyone and they can no longer understand the concepts he wants to discuss.
Charlie goes to a local diner and the bus boy drops and breaks several dishes. People, including Charlie, 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 he will use his brilliance to help Nemur and Strauss with the experiment. As he is working, Algernon bites Charlie, the first sign that the mouse is becoming disturbed and vicious. Burt tells Charlie that he is also becoming less cooperative and has less motivation to work. Charlie gets his own lab and comes up with The Algernon-Gordon Effect, which states that artificially increaed intelligence deteriorates at a rate of time directly proportional to the quantity of the increase. Algernon dies shortly after he finishes his paper. He dissects his brain and finds smoother lobes and decreased brain weight, which supports his hypothesis. Charlie buries Algernon in the backyard and puts flowers on his grave once a week.
Charlie begins to get really bad headaches and refuses to see Ms. Kinnian or the doctors. He does not want them to fell bad for him now that he is regressing to his previous state of low intelligence like Algernon had. He goes back to work for Mr. Donnegan at the factory and Joe and Frank defend him from other workers' jests and insults. Charlie accidently goes back to night school and Ms. Kinnian leaves crying. Charlie realizes that he is the reason for her being upset and leaves before she comes back to the classroom. Charlie decides to leave New York to have a new life and requests that someone put flowers on Algernon's grave.
