Flowers for Algernon by Daniel Keyes tells the story of a mentally impaired young man with a very low IQ named Charlie Gordon. He receives the opportunity to participate in a surgical experiment to dramatically increase his intelligence. The relationship conflicts with Miss Kinnian, Dr. Nemur, Dr. Strauss, and other characters all stem from Charlie's change after the experiment is successful. Before the experiment, Charlie is easy-going and compliant, with the eagerness to please of a young child. After the experiment, Charlie becomes a fully-functioning highly intelligent adult with a mind of his own.

Before Charlie's dramatic intelligence improvement, Miss Kinnian is his teacher at the Beekman College Center for Retarded Adults. Their relationship is strictly student-teacher. She recommends Charlie for the experiment because of her sympathy for his strong desire to improve. After the operation, Miss Kinnian continues to mentor Charlie, but as his mental prowess and self-awareness increase, he realizes that he has romantic feelings for her. This along with Miss Kinnian's desire to keep their relationship professional creates conflict. Further conflict is generated as Miss Kinnian begins to yield, but Charlie realizes that he will soon revert to the low level of intelligence that he had before the experiment.

The conflict in Charlie's relationships with Dr. Nemur and Dr. Strauss stem from the fact that the scientists are unable to see Charlie as anything other than a compliant laboratory subject. Their condescension prevents them from acknowledging Charlie's humanity and distinctiveness as an individual after the experiment drastically improves his mental and emotional acuity. This conflict continues even as Charlie's intelligence surpasses theirs, and he is able to discover a flaw in the hypothesis that led to the experiment which proves that he will eventually revert to his pre-enhanced state.