Flowers for Algernon tells the story of Charlie Gordon, a retarded man who, due to his passion for learning to read, is given the opportunity to participate in an experiment that will greatly increase his intelligence. The experiment has already had good results on a mouse named Algernon, and with the permission of his estranged sister, Charlie decides to undergo the surgery.

The entire book is told from the perspective of Charlie, through a series of progress reports he writes for the sake of the experiment. Rapidly, we see that the experiment is successful as the progress reports become easier to read and the spelling and vocabulary improve. Charlie"s intelligence increases exponentially, and the changes begin to frighten those in the bakery where he has worked for years. Eventually, they force him out, at which point Charlie begins to formalize his learning at the college where the experiment was done.

He absorbs many languages and fields of study quickly, as well as releasing numerous repressed memories. Though Charlie"s intellect develops rapidly, emotionally he remains stunted in many ways. Numerous attempts to develop a relationship with Alice, the teacher that recommended him for the surgery, are halted by panic attacks caused by repressed memories. Charlie also begins to realize that those he thought were his friends were really just laughing at him, and he begins to develop a more cynical outlook on humanity. He also begins to look down upon the other "intellectuals" he meets when he finds that their limited scope of study renders them incapable of viewing the world as comprehensively as he can.

Eventually, it becomes evident that not all is well with Algernon, and that the changes may not be permanent (a possibility from the beginning). Charlie takes it upon himself to discover the mistakes the lead on the experiment, Dr. Nemur, made and, if it is possible, to salvage his own intelligence. Charlie discovers that by rapidly increasing all the mental faculties of a person it is inevitable that they brain becomes worn out and will ultimately deteriorate as quickly as it developed.

As Charlie begins to deteriorate he meets with his mother and sister, finds some closure with his past, and is able to have a brief, yet fulfilling relationship with Alice. Algernon dies, and Charlie buries him in the backyard where he places flowers periodically. Slowly, the progress reports begin to regress in terms of spelling, punctuation, and vocabulary and Charlie realizes he must commit himself to a facility that is able to handle the mentally retarded so that he does not remind those who care about him of how far he has fallen. The book concludes with a request from Charlie that someone place flowers on Algernon"s grave.