After Charlie's operation to enhance his intelligence, he continues his work as a janitor at Donnegan's Plastic Box Company.
His co-workers don't know what has happened to him and grow frightened and wary because of his increased intelligence. Finally, he has to resign from the company when the owner, Mr. Donnegan, shows him a petition signed by every employee at the company except Fanny. Eight hundred and forty people have demanded that he be fired.
When Charlie seeks out Fanny to ask her about this, she explains that he is no longer an "ordinary" and "honest" man in the eyes of the other workers because of the sudden increase in his intelligence. When Charlie asks why it is a problem for a person to become more educated and knowledgable, Fanny likens it to Eve eating the apple offered to her by the serpent in the Garden of Eden, implying that what Charlie has done is evil. Charlie himself says that he feels shame over his newfound intellect because it has divided him from the people he knew and loved. He also feels caught between the proverbial rock and a hard place: when he was mentally disabled he was ridiculed, and now he is hated.
At first, Charlie doesn't realize how intelligent he has become. He tells Miss Kinnian,
I don't feel intelligent. There are so many things I don't understand.
However, his expectations are soon fulfilled as he surpasses everyone around him in intellectual achievements—at least until he realizes that the experiment is a failure, and he will lose what he has gained.