Charly is an adult male with a cognitive disability, struggling to survive in the modern world. His frequent attempts at learning, reading and writing prove difficult, and he is the subject of cruel pranks at the bakery where he does minor janitorial work. His teacher, Mrs. Kinnian, enrolls Charly in a clinical study where he is observed by a surgeon and a psychologist who have Charly "race" a mouse named Algernon, solving mazes. Algernon is usually the winner, thanks to an experiment involving brain proteins that greatly raised his intelligence. The experiment proceeds with surgery on Charly, who at first does not seem affected. However, he quickly becomes more logically advanced, soon becoming a pure genius. Emotional and intra-personal consequences are involved as Charly and his teacher become increasingly attached to one another. But when Charly gradually suspects the consequences of the experiment, he struggles with whether or not the procedure was a good idea.