Charlie Gordon experiences an enormous emotional change during the course of the story "Flowers for Algernon." While his intellectual development is clearly documented--Charlie's vocabulary increases and he is able to understand complex scientific information--readers need to infer what impact this same development has on his emotions. As Charlie gains understanding of the world and his place within it, he realizes that he had been treated poorly and inhumanely by those people he thought were friends.
An example of this is the way in which he is treated by his colleagues at the bakery. Before Charlie's intellect changes, he does not realize that these men are not his friends and that they spend time with him as a form of amusement for themselves. Charlie does not realize that he is being used as a clown or jester, and he believes that they are laughing with him, not at him. As Charlie's intellect grows, he sees things as they truly are, and he understands that he has been mistreated and used. He feels hurt and wounded by this.
In addition, Charlie's emotions are impacted when he finds himself having strong romantic feelings for his teacher, Ms. Kinnian. Before the procedure Charlie viewed Ms. Kinnian as a friend and mentor. She was his teacher in a special education class. Once he begins to understand who he is and who he used to be, he sees more in Ms. Kinnian and becomes emotionally involved with her. He falls in love with his teacher and desires a romantic relationship.