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Flowers for Algernon, written by Daniel Keyes, follows a man, Charlie, and a mouse, Algernon whose IQs have been artificially increased. Originally published as a short story, Flowers for Algernon was inspired by several events in Keyes’ life, including his experience teaching English to developmentally disabled students.

In a series of progress reports, Charlie Gordon, an ambitious, developmentally disabled 32-year-old, chronicles his candidacy for an experimental operation, led by Dr. Strauss and Professor Nemur, that would allegedly “make him smart.” Burt, a graduate student working on the experiment, introduces Charlie to another participant: a white mouse named Algernon who completes a maze in record time. Charlie races against Algernon, completing the same maze on a piece of paper, and Algernon wins. Charlie is selected for the experiment and his operation goes smoothly, but he’s frustrated when he's not immediately brilliant.

After some time off for his operation, Charlie returns to the bakery where he works as a janitor. With the help of a TV-like machine that Nemur and Strauss tell him to turn on while he sleeps, Charlie begins to learn and remember things from his childhood, and he finally beats Algernon in a maze race. Charlie’s bakery co-workers, Frank and Joe, try to play a trick on him, but it backfires, and Charlie gets promoted instead. Charlie begins to understand that his so-called friends at the bakery are making fun of him.

Charlie initially learned about the experiment through Alice Kinnian, who teaches a class at Beekman for developmentally disabled adults that Charlie used to attend. Charlie now invites Alice to a movie and dinner and confesses his feelings for her, but she rebuffs him, saying it wouldn’t be appropriate for them to be together… for now. After realizing a bakery co-worker is stealing, Charlie approaches Alice again, asking for her advice and this time saying that he loves her. She agrees to go on a date with Charlie and he tries to kiss her, but he pulls back when he thinks he sees a boy watching them. Charlie gets fired from the bakery because his sudden intelligence has spooked his co-workers, and he feels alone.

The research team presents their findings at a convention, revealing that at the peak of Algernon’s intelligence, his behavior became erratic. Charlie, now more intelligent than the scientists, realizes that they missed something, and he may not have as much time as he thought. He also finds the conference demeaning, especially Nemur’s continued implication that he did not think of Charlie as a human being before the operation. Charlie releases Algernon from his cage and, after a conference-wide search for the mouse, stows Algernon away in his pocket and heads back to New York in secret.

Charlie visits his father, Matt, at the barbershop where he works. Charlie looks forward to reconnecting, but when he arrives at the barbershop, his father, who hadn’t seen him since he was a child, doesn’t recognize him. Charlie decides not to reveal his identity, afraid his father will resent his newfound intelligence, like others have.

Charlie rents a new apartment so the research team can’t find him and gets close with Fay, his across-the-hall neighbor. Fay brings over a female mouse companion for Algernon and a bottle of gin for Charlie, and she and Charlie get drunk together. The next morning, Fay explains that, when he was drunk, Charlie put on what she calls “a moron act,” and Charlie realizes his pre-surgery self is still with him. After a night out alone in the town where he sees a developmentally disabled boy get mocked, Charlie vows to worry less about himself and focus more on helping others.

Charlie visits Alice at her apartment and she’s thrilled to see him. He tries to make love to her, this time imagining that she’s Fay, but the old Charlie – the same boy he hallucinated the last time he tried to kiss Alice – won’t let him. Charlie buys some gin, goes home, and successfully sleeps with Fay.
After seeing signs that Algernon is deteriorating, Charlie returns to the lab and gives Algernon back to Nemur, Strauss, and Burt. The funders of the experiment, The Welberg Foundation, have authorized Charlie to conduct his own research and Nemur reluctantly shares the lab’s resources. Charlie notices the incinerator used to dispose of failed lab subjects and makes Burt promise that if the worst should happen to Algernon, they’ll give him to Charlie to keep, rather than disposing of him in this way. Charlie wonders about contingency plans for himself, should he regress. Nemur explains that the Foundation has arranged to send him to the Warren State Home, an institution dedicated to caring for developmentally disabled people, if it comes to that.

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