Flowers for Algernon is told as a series of “Progress Reports” written by Charlie Gordon, a 32-year-old man with an IQ of 68. As Keyes’s novel opens, Charlie has volunteered to be the subject of an experimental surgical procedure that would more than triple his IQ. Although Charlie is of subnormal intelligence, he is unusually motivated, taking night school classes at the Beekman University Center for Retarded Adults. At first, he is afraid he won’t be chosen for the project. He doesn’t understand what to do when he is asked to tell what he sees in inkblots, and when he traces through a diagram of a maze in competition with Algernon, a mouse who is running an actual maze, Algernon always wins. Nonetheless, Charlie is chosen by the scientists in charge of the project-Professor Nemur, the psychologist who developed the technique, and Dr. Strauss, the neurosurgeon who performs the actual operation. After the surgery, Charlie returns to his job as a janitor at Donner’s Bakery, where nobody is aware of his operation.

The sad state of Charlie’s life prior to the surgery is made clear when Joe Carp and Frank Reilly, whom Charlie regards as his friends, take him out to a bar, get him drunk, make fun of him, and leave him to find his way home.

As time passes, however, it becomes obvious that Charlie is getting smarter. At the bakery, he successfully operates a complicated machine that mixes baking dough. His performances on the psychological tests improve, and he finally beats Algernon at running the maze-a significant development, as the mouse has had its intelligence raised by the same surgical procedure that Charlie underwent. And his Progress Reports are increasingly more sophisticated and articulate than before.

As Charlie’s IQ increases, so does his awareness of himself and others. Now, when his “friends” make fun of him, he understands their true motivations. He steadily advances at work, but takes no satisfaction from it because the other employees resent him. Eventually, his coworkers at the bakery are so unnerved by his unexplained changes that they sign a petition demanding that he be fired. The only person who doesn’t, an old woman named Fanny Birden, nonetheless thinks Charlie’s condition “ain’t right” and wishes he could return to “the good simple man” he had been.

Charlie also realizes that he has fallen in love with Alice Kinnian, the night school teacher who originally recommended him for the operation. Despite the gentleness of her rejection, Charlie is terribly upset, as he is when he catches Gimpy, the one person at the bakery who had been kind to him, stealing. Charlie is becoming aware that factual knowledge and intellectual ability may not prepare a person to deal with all of life’s problems.

As Charlie tries to cram a lifetime of intellectual and emotional development into a period of months, he also increases his self-awareness by recovering lost memories, a process triggered by sleep-learning devices and continued through his ongoing psychotherapy sessions with Dr. Strauss. Through a series of flashbacks, we learn the agonizing details of Charlie’s early life. Charlie’s father, Matt, tried to do the best he could for his son. But Charlie’s mother, Rose, denied that there was anything “wrong” with him and beat him when he was unable to learn like other children. However, when Charlie’s sister Norma was born with normal intelligence, Rose turned against Charlie and sought to “protect” Norma from him, reacting with particular violence to anything he did that showed his developing sexuality. Finally, after a hysterical outburst in which Rose threatened to kill Charlie, Matt took Charlie to live with his uncle Herman. When Herman died several years later, Rose tried to have Charlie committed to the Warren State Home and Training School, an institution for the mentally handicapped, but Charlie avoided this when the owner of Donner’s Bakery, a lifelong friend of his uncle Herman, offered him a job. The “new” Charlie now realizes that both his extraordinary motivation to learn and his confused responses to women are rooted in how he was treated by his mother.

As Charlie’s IQ surges to nearly triple its original level, his relationship with Alice deepens, but when she is finally able to return his feelings, his childhood traumas leave him unable to make love to her. More importantly, the gap between their respective IQs makes it harder and harder for them to communicate, a problem the genius Charlie now has with almost everyone. In particular, he has come to regard Nemur and Strauss, who previously seemed unapproachable geniuses, as narrowly-focused specialists more interested in acquiring fame and power than they are in increasing knowledge and helping others. When Nemur and Strauss take Charlie and Algernon to a psychologists’ conference in Chicago to announce the success of their procedure, Charlie is outraged by their treating him like an object on display rather than as a human being. He is also disturbed by what appears to be an error in Nemur’s analysis of the “waiting period” after the operation. Disgusted, Charlie deliberately lets Algernon loose in the conference room. While the others are frantically trying to recover the mouse, Charlie slips Algernon in his pocket, leaves the conference, and returns to New York, where he rents an apartment and drops out of sight.

Now completely on his own, Charlie devotes himself to reading, thinking, and recovering his memories. During this time he forms a relationship with Fay Lillman, a painter who lives down the hall. Charlie is attracted to Fay’s free spirit and lack of inhibitions, but, as with Alice, he is unable to have a sexual relationship with her. His sense of isolation increases. Yearning for meaningful contact with others, he walks the streets of New York feeling an “unbearable hunger” for human contact. He even goes to visit his father, who left his mother several years earlier. His father fails to recognize him, and Charlie cannot bring himself to reveal his identity. A few days later, while dining alone in a restaurant, Charlie witnesses a young man drop a stack of dishes: When the owner came to see what the excitement was about, the boy cowered-threw up his arms as if to ward off a blow. “All right! All right, you dope,” shouted the man, “don’t just stand there! Get the broom and sweep up that mess. A broom … a broom! you idiot! It’s in the kitchen. Sweep up all the pieces.” When the boy saw that he was not going to be punished, his frightened expression disappeared, and he smiled and hummed as he came back with the broom. A few of the rowdier customers kept up the remarks, amusing themselves at his expense.
“Here, sonny, over here. There’s a nice piece behind you…”
“C’mon, do it again…”
“He’s not so dumb. It’s easier to break ’em than to wash ’em….”
As the boy’s vacant eyes moved across the crowd of amused onlookers, he slowly mirrored their smiles and finally broke into an uncertain grin at the joke which he did not understand. I felt sick inside as I looked at his dull, vacuous smile-the wide, bright eyes of a child, uncertain but eager to please, and I realized what I had recognized in him. They were laughing at him because he was retarded.
And at first I had been amused along with the rest.
Suddenly, I was furious at myself and all those who were smirking at him. I wanted to pick up the dishes and throw them. I wanted to smash their laughing faces. I jumped up and shouted: “Shut up! Leave him alone! He can’t understand. He can’t help what he is … but for God’s sake, have some respect! He’s a human being!”

The incident makes Charlie decide to return to Beekman University and work on his own to perfect Nemur and Strauss’ procedure so that it might help others like himself.

After returning to the University, Charlie renews his relationship with Alice but is still unable to make love to her. He turns back to Fay, whom he does not truly love but with whom he is able, finally, to have a sexual relationship. Eventually, though, Charlie becomes so immersed in his research that he moves into the lab and breaks off with Fay, who resents the time he devotes to his work-and who also has never known the truth about Charlie. Time is of the essence, as Algernon is beginning to show signs of instability and decline. Charlie works feverishly to determine if the effects of his operation will last, driven both by his fear of reverting to his former self and his desire to find any information at all that might help other mentally handicapped people. He also begins to achieve a more mature insight into his own nature and that of other people. In a confrontation with Nemur, Charlie declares that “intelligence and education that hasn’t been tempered by human affection isn’t worth a damn.”

Finally, Charlie completes his research. In a letter to Nemur, he announces his discovery of the “Algernon-Gordon Effect”: “artificially-induced intelligence deteriorates at a rate of time directly proportional to the quantity of the increase.” Charlie will revert to his former IQ within a matter of months. Shortly after this discovery, Algernon dies.

Faced with the prospect of losing all he has gained, Charlie seeks to come to terms with himself and his memories. He visits his mother and sister, who still live in Brooklyn. Rose has sunk into senility and only momentarily recognizes her son. Norma, far from being the hateful rival Charlie remembers, is a kind and intelligent woman who sincerely regrets both Charlie’s hardships and her own inability to help him through them.

Charlie also comes to terms with Alice Kinnian, who is determined to stick by him as long as possible. Having put the ghosts of his past to rest, he is finally able to make love to her, and they are fully together for a brief time. But Charlie’s decline is rapid, and he pushes Alice away before he completely reverts to his former self.

Charlie’s final Progress Reports reflect his rapid deterioration as his writing reverts to its earlier semi-literacy. However, he has retained some memory of his experiences, and perhaps some insight as well. When he goes back to his old job at the bakery, he notes, “if they make fun of you don’t get sore because you remember their not so smart like you once thot they were.” The bakery workers accept him back; Carp and Reilly, who formerly had tormented Charlie, defend him when a new worker makes fun of him. However, Charlie finally decides to leave New York for good and check himself into the Warren State Home and Training School. His final Progress Report, dated only eight months after the first, asks that someone “put some flowrs on Algernons grave in the bak yard.”

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