The narrative is told in the first person and is made up of reports written by the main character.
Charlie Gordon, 32, who is mentally retarded, lives in New York City and works as a janitor in a private bakery where his uncle has placed him. He barely remembers his parents and younger sister. Charlie goes to a special school where his teacher, Alice Kinnian, teaches him to read and write.
One day Miss Kinnian brings him to Professor Nemours and Dr. Strauss. They are conducting an experiment to increase intelligence, and they need a volunteer. Miss Kinnian proposes Charlie, the most capable student in her group. Charlie has wanted to be smart since childhood and willingly agrees, even though the experiment involves a risky operation. Strauss, a psychiatrist and neurosurgeon, tells him to write down his thoughts and feelings in the form of reports. Charlie's first reports are full of mistakes.
Charlie begins to take the standard psychological tests, but he fails. Charlie is afraid he won't fit in with the professor. Gordon meets mouse Algernon, who has already had surgery. The test subjects race through the maze, and Algernon is faster each time.
On March 7, Charlie undergoes surgery. Nothing happens for a while. He continues to work in the bakery and no longer believes he will become intelligent. The bakery workers make fun of Charlie, but he understands nothing and laughs with those he considers friends. He tells no one about the operation, and he goes to the lab every day to do tests. On March 29, Charlie passes the maze faster than Algernon for the first time. Miss Kinnian begins working with him individually.
On April 1, the bakery workers decide to play a joke on Charlie and make him turn on the dough mixer. Suddenly Charlie succeeds, and the owner promotes him. Gradually Charlie begins to realize that to his "friends" he is just a clown who can be pranked with impunity and malice.
I have reached a new level of development. But anger and suspicion were the first feelings I had for the world around me.
He recalls the most hurtful incidents, becomes bitter, and stops trusting people. Dr. Strauss conducts psychotherapy sessions with Charlie. Although Gordon's intelligence increases, he knows very little about himself and is still emotionally a child.
Charlie's past, previously hidden from him, begins to come to light.
I'm like a man who slept half his life and now tries to find out who he was while he was asleep.
By the end of April, Charlie changes so much that the bakery workers begin to be suspicious and hostile toward him. Charlie is reminded of his mother. She did not want to admit that her son was born mentally retarded, beat the boy, and forced him to attend regular school. Charlie's father tried unsuccessfully to protect his son.
Charlie is in love with his former teacher, Alice Kinnian. She is not at all as old as Charlie thought she was before the operation. Alice is younger than he is, and he begins an inept courtship. The thought of a relationship with a woman terrifies Charlie. The fault lies with his mother, who feared that her mentally retarded son would hurt his younger sister. She drummed into the boy's head that women should not be touched. Charlie has changed, but the subconscious taboo still applies.
Charlie notices that the senior cook of the bakery is stealing from the owner. Charlie warns him, threatening to tell the owner, and the theft stops, but the relationship is permanently damaged. This is the first major decision Charlie has made on his own. He learns to trust himself. Charlie is pushed to his decision by Alice. He confesses his love for her, but she realizes that the time for such a relationship has not yet come.
The bakery owner was a friend of his uncle's, promised to take care of Charlie, and he kept his promise. Now, however, Charlie is strangely changed, the workers are afraid of him and threaten to quit if Charlie stays. The owner asks him to leave. Charlie tries to talk to his former friends, but they hate the fool who is suddenly smarter than them all.
Reason drove a wedge between me and everyone I knew and loved, kicked me out of the house. I've never felt so alone.
Charlie's been out of work for two weeks. He tries to escape his loneliness by embracing Alice, but nothing works. It is as if Gordon sees himself and Alice from the outside, through the eyes of the old Charlie, who becomes terrified and does not allow them to finally come together. Gordon remembers how his sister hated and was ashamed of him.
Charlie gets smarter and smarter. Soon those around him no longer understand him. This causes him to quarrel with Alice, who feels like a complete fool around him. Charlie distances himself from everyone he knows and immerses himself in his studies.
On June 10, Professor Nemours and Dr. Strauss fly to a medical symposium in Chicago. The main "exhibits" at the big event are Charlie and Algernon the mouse. On the plane, Charlie recalls how his mother tried, to no avail, to cure him, to make him smarter. She spent almost all the family savings that his father, a hairdressing equipment salesman, wanted to open his own barbershop with. His mother left Charlie alone, giving birth once more and proving she was capable of having healthy children. Charlie, on the other hand, dreamed of turning into a normal person so that his mother would finally love him.
Every day I learn something new about myself, and the memories, which started with a little ripple, overwhelm me in a ten-point storm.
At the symposium, Charlie discovers such vast knowledge and high intelligence that the professors and academics pale in comparison to him. This does not prevent Professor Nemours from calling him "his creation," equating Charlie with Elgernon the mouse. The professor believes that before the operation, Charlie was an "empty shell" and did not exist as a person. Many people think Charlie is arrogant and intolerant, but he just can't find his place in life. At a report on intelligence enhancement surgery, Gordon feels like a guinea pig. In protest, he lets Algernon out of his cage, then finds him first and flies home.
In New York, Gordon sees a newspaper with a picture of his mother and sister. He recalls how his mother forced his father to take him to an orphanage. After giving birth to a healthy daughter, her mentally retarded son caused her nothing but disgust.
Charlie rents a four-room furnished apartment near the library. In one of the rooms, he sets up a three-dimensional maze for Algernon. Charlie doesn't even tell Alice Kinnigan about his whereabouts. Soon he meets his neighbor, a freelance artist. To get rid of his loneliness and make sure of his ability to be with a woman, Charlie enters into a relationship with his neighbor. The old Charlie doesn't interfere with the relationship because he doesn't care about the woman, he only observes from the sidelines.
Charlie finds his father, who has divorced his wife and opened a barbershop in a poor neighborhood. He doesn't recognize his son, and he hesitates to open up. Gordon discovers that after drinking heavily, he turns into a mentally retarded Charlie. Alcohol unleashes his subconscious, which has not yet caught up with his rapidly growing IQ.
Nothing in us disappears without a trace. The surgery has covered Charlie with a thin layer of culture and education, but he remains. He watches and waits.
Now Charlie tries not to get drunk. He takes long walks, stops at cafes. One day he sees the waiter, a mentally retarded guy, drop his tray of plates, and the customers start making fun of him.
It's amazing how people of high moral principle ... never allowing themselves to take advantage of someone born without arms, legs, or eyes ... laugh easily and thoughtlessly at someone born without a mind.
This prompts Gordon to continue his scientific work to benefit such people. Having made up his mind, he meets Alice. He explains that he loves her, but a little boy, Charlie, who is afraid of women because his mother used to beat him, comes between them.
Charlie starts working in the lab. He has no time for his mistress, and she leaves him. Algernon begins to have incomprehensible bouts of aggression. At times he cannot pass his maze. Charlie takes the mouse to the laboratory. He asks Professor Nemours what they were going to do with him if he failed. It turns out that Charlie was destined for a place at the Warren Public Social School and Sanitarium. Gordon visits this institution to know what awaits him.
Algernon gets worse and refuses to eat. Charlie, on the other hand, peaks mentally.
It's as if all the knowledge I've gained in the last few months has come together and lifted me to the pinnacle of light and understanding.
On August 26, Gordon finds an error in Professor Nemours' calculations. Charlie realizes that he will soon begin to have a mental regression, just like Algernon. On September 15, Algernon dies. Charlie buries him in the backyard. On September 22, Gordon visits his mother and sister. He discovers that his mother is senile. His sister has a hard time with her, and she is glad Charlie found them. The sister had no idea that her mother had gotten rid of Charlie for her. Gordon promises to help them as long as he can.
Gordon's IQ declines rapidly and he becomes forgetful. Books, once beloved, are now incomprehensible to him. Gordon is visited by Alice. This time, the former Charlie does not prevent their love. She stays for a few weeks, courting Charlie. Soon he drives Alice away-she reminds him of powers that cannot be returned. More and more mistakes appear in the reports Charlie still writes. Eventually they become the same as they were before the operation.
On November 20, Charlie returns to the bakery. The workers, who used to bully him, now patronize and protect him. However, Charlie still remembers that he was smart. He does not want to be pitied, so he goes to Warren. He writes a farewell letter to Miss Kinnian, asking him to put flowers on Algernon's grave.