Charlie's desire to have the surgery stems from his desire to have friends. Consider this quote from the book:

I dont care so much about beeing famus. I just want to be smart like other pepul so I can have lots of frends who like me.

Charlie has always been isolated and alone. People may be nice to him, but no one is his friend. Even his family members do not bond with him the way they do with each other. His disability keeps him separated from other humans.

When he "gets smart," it is the same problem. He is isolated because of his genius. He is taken to a scientific convention to be shown off--like a circus act. Algernon represents the only living being that has experienced what Charlie has experienced. Algernon is also the circus act. He may not be able to understand or feel that the way Charlie does, but it makes Algernon the one creature with which Charlie does feel bonded. If he did not feel that bond, he would not have foreseen his own future.

Algernon and Charlie undergo the same operation to enhance their intelligence. Charlie is the first human subject of this experiment and by watching the changes in Algernon's intelligence and behavior he is better able to understand his own progress after the operation.  Sadly, once Charlie figures out that the operation will eventually self-reverse, Algernon's mental capacity begins to deteriorate before his own, providing Charlie with a grim preview of what is in store for him.  Algernon's behavior, along with Charlie's, becomes more and more erratic.  Eventually Algernon dies, while Charlie fully regresses back into his original mental retardation.  However, Charlie is still able to remember what happened.  Unable to bear the emotional pain this causes him, he checks himself into a state facility where no one knows about the experiment.  In a final letter to Alice he asks her to put flowers on Algernon's grave.

In Flowers for Algernon by Daniel Keyes, what happens to Algernon and how does it effect Charlie?

Sadly, Charlie discovers that the amazing increase in Algernon's intelligence, and thus in his own, is only temporary.  Shortly after, Algernon dies, and knowing that his own intellectual demise is forthcoming, Charlie begins to tie up loose ends.  He visits his mother, who barely remembers him, makes peace with his sister, finally ending what had many years ago been an antagonistic relationship, and spends time with his ever-faithful friend and former teacher, Alice Kinnian.  Charlie indicates at the end that he is going away, although it is not clear if that means he is leaving New York, or planning a suicide.  This ending, while ambiguous, is completely consistent with the theme Keyes has woven throughout the work of a man's alienation from society.