The theme of intelligence in Flowers for Algernon explores the complexities and consequences of artificially enhanced intellect. The protagonist, Charlie Gordon, undergoes a surgical procedure that temporarily boosts his intelligence, allowing him to experience life as a genius. This transformation brings both opportunities and challenges, ultimately leading to a poignant exploration of the nature of intelligence and its impact on human relationships and self-awareness.

Charlie's surgery results in a significant increase in his intellectual capabilities. He learns multiple languages, excels in mathematics, and expands his vocabulary. This newfound intelligence allows him to form a mature relationship with Miss Kinnian, his former teacher, and engage in scientific research. However, the enhancement also brings awareness of the limitations and ethical shortcomings of those around him. Charlie realizes he has been used as a "lab rat" by researchers more interested in their own success than his well-being.

The relationship between Charlie and Miss Kinnian evolves as his intelligence grows. Initially, she is his teacher, but as he surpasses her intellectually, their dynamic shifts to one of romantic interest. Miss Kinnian fears that Charlie's rapid intellectual ascent will leave her behind, making a long-term relationship impossible. Her concerns are valid, as Charlie's intelligence eventually regresses, complicating their relationship further. She expresses her fears, stating, "I can see only a little bit of that, Charlie, and I won't go much higher than I am now, but you'll keep climbing up and up, and see more and more, and each step will open new worlds that you never even knew existed."

The temporary nature of Charlie's intelligence highlights the emotional toll of such a transformation. As his cognitive abilities decline, he becomes acutely aware of the impending loss and the return to his original state. This awareness is a double-edged sword; while intelligence brings insight and understanding, it also exposes him to the harsh realities of his situation. The statement "The more intelligent you become, the more problems you'll have, Charlie" underscores the idea that increased awareness often leads to greater emotional burden.

Charlie and Algernon, the lab mouse, share a parallel journey of intelligence enhancement and decline. Both experience the temporary benefits of increased intellect, only to face the inevitable regression. This shared experience emphasizes the fleeting nature of artificial intelligence and the profound impact it has on both characters. Charlie's awareness of his fate adds a layer of tragedy to his story, as he understands the full implications of his transformation and its reversal.