We look at the story through the “progress reports” of Charlie Gordon. He is the main character, the genius, the mentally retarded “lab rat” and a poor little boy who is afraid to love.
32-year-old Charlie Gordon is mentally retarded. He lives in New York working as a cleaner in a private Donner’s Bakery. But even this job wouldn’t be granted to him without the interference of his uncle trying to find a place in life for his nephew. Charlie remembers that once he had a family - parents and younger sister - but this memories are scarce and dim. The closest person he has now is Alice Kinnian, his teacher in the school for mentally challenged people, who teaches him to read and write. Charlie, whose mind is still a mind of a little boy in need of love and care, sees her as motherly figure.
Miss Kinnian really does care of Charlie. Once, when she learns that some scientists - professor Nemur and Dr. Strauss - are searching for a volunteer for their intelligence enhancing surgery and asks Charlie, as the most capable students of the group, if he wants to try. Charlie dreamt about becoming smart since his childhood and he gladly agrees, even despite the surgery can be risky. The psychiatrist and neurosurgeon, Dr. Strauss, tells him to write down his thoughts and sensations before and after the operation. The first reports of Charlie Gordon are short and clumsy with lots of mistakes.
Before the operation, Charlie undergoes some standard psychological IQ tests to define his initial level of intelligence. Charlie fails every time and he is very afraid that the professors will be displeased with his stupidity and will reject him as a volunteer. Charlie competes with the lab rat Algernon, which had the same surgery recently. The rat finds the end of the labyrinth faster than Charlie, each time.
The surgery is appointed to the 7th of March. But after it nothing happens for some time, Charlie stays at the same IQ level as before. He returns to the bakery, slowly losing hope that he ever become smarter. The bakery workers cruelly mock Charlie as they did from the very beginning of his career, but he doesn’t understand it and laugh with his “funny friends”. He doesn’t tell anyone about the operation, but he comes to the laboratory every day to pass the same tests. On March 29, Charlie completes the labyrinth test faster than Algernon. Miss Kinnian, seeing his progress, starts to teach him individually.
On 1st of April the bakery staff pulls a cruel joke, asking Charlie to turn on the dough mixer (this task can be dangerous for a mentally challenged person). Unexpectedly Charlie manages to do this without any problems and the owner of the bakery promotes him. The other bakery workers are not glad, actually they don’t see Charlie as a person, only as their personal jester, and think he doesn’t deserve the promotion. Charlie begins to understand this. His “friends” aren’t real friends, they are cruel and not very clever people who enjoy laughing at someone less smart than them.
Memory returns to Charlie. He starts understanding how cruel and unfair was this world to him. His first feelings in the new life were anger and suspicion. Dr. Strauss has a course of psychotherapy sessions with Charlie to help him integrate into the society, but he still leaves embittered. He understands that his intelligence may be rising, he may look as an adult, but inside, emotionally he is still an inexperienced child. The only friend he has is Alice Kinnian. To his surprise, she isn’t as motherly as he thought. Actually Alice is younger than him. The feelings Charlie has towards her slowly turn into romantic ones. Alice is delighted to see the progress of her former student, but she still feels awkward about the relationship development.
Charlie finally remembers his family. His mother couldn’t admit that her son is mentally retarded. She forced him to attend ordinary school and beated him, unable to express her despair in a different way. Charlie’s father tried to protect him but failed all the time. His mother gave birth to another child, a healthy girl, to prove that she can be a good mother and produce “proper” kids. She was afraid of Charlie harming the baby, so she steadily and strictly indoctrinated him not to touch women. Now Charlie is a grown up, smart and handsome man, but that little boy, frightened by his mother’s fury still stands between him and Alice.
At his work, Charlie notices that the cook steals money from the owner. Charlie feels that it is unfair, also he wants to protect the man who gave him the first and only job in his life. He threatens the cook to tell the owner, the thefts are stopped, but now the bakery workers openly dislike Charlie for not following their inner social rules. But Charlie doesn’t need their approval anymore, he slowly learns to trust himself and be confident. Alice supports him on his way. Finally, Charlie finds courage to confess to her, but she kindly turns him down, saying that love needs time to develop.
The owner of the bakery is facing a hard dilemma. Charlie is the nephew of his friend and he promised to take care of him, but other workers threatened him to leave at once if Charlie isn’t fired. The bakery owner is very sorry, but he asks Charlie to leave. Charlie tries to talk to former friends but they utterly hate their “jester” who suddenly became a better and smarter person than all of them.
Charlie doesn’t work for two weeks and he doesn’t know what to do with his newfound freedom. He tries to escape the loneliness with Alice but it doesn’t work - he still sees her with the eyes of the little boy who isn’t allowed to touch women. Gordon remembers that his sister hated him, was ashamed and frightened of him and this thought just adds more to his depression.
His intelligence grows dramatically. Soon no one understands him - Charlie is now a genius. It’s harder and harder to get along with Alice who feels herself stupid near him. Understanding that he upsets her constantly, Charlie secludes himself from anyone he knows and starts educating himself.
At June 10 Professor Nemur and Dr. Strauss attend a medical symposium in Chicago and take Charlie with them. He doesn’t object, hoping that this event, where the brightest minds are present, may help him to defeat his loneliness. He flies with both scientists and his fellow rat Algernon. In the plane, Charlie remembers another thing from his childhood: his mother spent almost everything that family had to his treatment, desperately trying to make him smarter. She spent all the savings that his father gathered to open his own business. Finally, she gave up and then gave birth to another child, leaving Charlie alone. Charlie now is even more driven to become “normal” and meet his mother to prove that she still can love him.
At the symposium Charlie is one of the brightest speakers with his vast knowledge and high intelligence. Even the professors are amazed by him, feeling pale in comparison. But this doesn’t prevent professor Nemur to talk of him as of inanimate object or another lab rat like Algernon. He calls Charlie “his creation” in his presence and sure that Charlie was just an empty shell before his surgery. Charlie rudely objects this. Many people find him arrogant and intolerant, but he isn’t just used to the society norms and double morality, so he tells what he really thinks and feels. He now feels himself like just another animal for experiments. As protest, he frees Algernon from his cage and buys a ticket, flying home with the rat.
Back in New York Charlie sees a newspaper with a photo of his mother and sister. He has another flashback in which his mother forced his father to take Charlie to the orphanage, because she thought he is a disgusting obstacle for the family with a healthy daughter.
Charlie rents an apartment near the library he attends. In one of the rooms he arranges a huge three-dimensional labyrinth for Algernon. He doesn’t tell anyone where he is, even Alice Kinnigan doesn’t know about it. He starts courting his neighbour, an artist, just to prove himself he can be with women. This woman means nothing to him, they aren’t emotionally close, so his inner boy doesn’t object. He just observes what is happening from inside of the mind of grown-up Charlie.
Charlie finds his father who divorced his mother and finally opened his own business - a hair salon in the poor district of New York. Charlie also discovers that he shouldn’t drink alcohol, because he turns back into mentally retarded Charlie when drunk. His conscious is still the same, though his IQ is overwhelming.
Once he sees a mentally challenged waiter in the cafe - a man who behaves like Charlie himself before. But he accidentally drops a tray with plates on it and visitors begin laughing at him as cruelly as bakery workers laughed at Charlie. Charlie is disgusted and surprised. He understands that people can consider themselves being of high moral principles, they may never allow themselves to take advantage of a man born without hands, feet or eyes, but they still don’t see mentally ill people as people, only as laughingstocks.
But this time it just solidifies the decision to continue researches to benefit such people as he was before. Charlie gathers all his courage and meets Alice. He again explains that he loves her very much, but the little boy abused and beaten by his mother, will always stand between them.
Charlie starts working in the lab, continuing Nemur’s studies. He doesn’t have time for his lover anymore, so she goes. The only living being Charlie communicates with is Algernon, the rat. But soon Charlie notices that Algernon starts being aggressive without purpose and sometimes he can’t pass his labyrinth test. Soon he gets worse, refuses to eat and eventually dies. Charlie cries for him but finally gives him a proper burial in the garden.
Charlie reaches the peak of his intelligence. On August 26, he finds a mistake in Nemur’s calculations that he names the “Algernon-Gordon Effect”. Due to his studies, the intelligence of a being that experienced mentally enhancing surgery will soon decrease as rapidly as it increased. He asks professor Nemur what they were going to do to him in case of failure. Nemur answers that Charlie would be transferred into the psychiatric ward. Charlie visits this institution to learn what is waiting for him.
Gordon tries to spend the rest of his life meaningfully. He visits his mother and sister just to discover that his mother has developed dementia and now is in even more pathetic state than he was. His sister cares for her but she is exhausted with this. She didn’t know that their mother got rid of her brother. Charlie promises to help them while he is able.
His IQ is getting lower, Charlie becomes forgetful. He spends time with Alice, their love is short, bittersweet and passionate. But when Charlie feels that his old self is about to return, he asks her to leave. Alice is again smarter than him, he can’t stand seeing her as the embodiment of the mental abilities he is losing. And also Charlie doesn’t want her to suffer seeing his regression.
Charlie returns to the bakery. The workers, content with his degeneration, are ready to take care of him and protect him. They even feel something alike to sympathy. But Charlie remembers everything that was too well. He doesn’t want to be neither mocked nor pitied. He writes a farewell letter to Alice (this letter has as many mistakes as before the surgery) asking her to bring flowers to Algernon’s grave. Charlie sends the letter and voluntarily goes to psychiatric ward.