Charlie Gordon, 32 years old and developmentally disabled with an I.Q. of 68, has been chosen for an experimental surgery to increase his intelligence. The procedure has already worked on a mouse called Algernon, and the doctors are optimistic that it will be successful for Charlie, too.
The surgery is a success, and Charlie’s intelligence skyrockets. However, he finds that his emotional intelligence hasn’t kept pace with his mental intellect. He realizes that he has been treated cruelly by his friends at the bakery, and others throughout his life.
Charlie leaves his job at the bakery because the others treat him strangely now, and with fear. They don’t understand the change that is happening in Charlie. Charlie learns so much information that he quickly surpasses his doctors. He develops a sense of affinity with Algernon, and feels increasingly alienated from the people he interacts with, including Alice.
Charlie is taken to a scientific convention in Chicago where he and Algernon are being showcased. Charlie becomes increasingly perturbed as they show films and pictures of him in early interviews, which he had not been aware of. He takes off with Algernon back to New York. Algernon soon begins to regress, and Charlie realizes he doesn’t have much time left.
Charlie and Algernon return to the lab, where Charlie continues his research. He ends his relationship with Fay. Algernon dies, and Charlie goes to visit his mother and sister. He finds his mother is senile, and his sister Norma is her caretaker. He and Norma reconcile, as Charlie knows he won’t be able to play the “big brother” role for much longer.
Charlie and Alice finally consummate their relationship before Charlie’s regression worsens. They spend a few weeks together before Charlie’s moods drive her away. His coordination, spelling, and grammar worsen. His final wish as he finishes his last progress report before going to live at the Warren Home is for someone to put flowers on Algernon’s grave.