Charlie Gordon has an IQ of 68; in the 1960s, this IQ level was classified as mentally retarded (what we would today refer to as "developmentally disabled"). Although a happy adult with a job at a bakery and friends, Charlie agrees to take part in an experiment recommended by Alice, his adult education teacher. Within a few short weeks after the surgery, Charlie's progress is dramatic. The book portrays many of the changes he undergoes by way of Charlie's written journal. The evolution of Charlie's spelling, vocabulary and complexity of thought indicate the success of the surgery in improving Charlie's intelligence. A white mouse named "Algernon" has the same surgery and is also subjected to some of the same tests that Charlie undergoes, to measure their improvement.
But Charlie's mental capacity is not the only thing that changes; his social and emotional intelligence also grows in leaps and bounds. He begins to understand that his fellow employees at the bakery where he worked had previously not been his "friends" but had made fun of him. He has never known mature love or affection for a woman before, but finds both of these with Alice. His intelligence surpasses even that of the doctors conducting the experiment. When it becomes clear that the effects are temporary, however (as evidenced by the decline in Algernon's health and intelligence), Charlie is distressed to realize that his new life, made richer by his newly-acquired intelligence, may not flourish for much longer.