At a psychological conference in Chicago, Charlie becomes upset. First, having become more intelligent that either of the doctors who engineered his heightened intelligence, he realizes their data is flawed. He and Algernon will rapidly lose the intelligence they had so rapidly gained. Further, he resents being treated like a lab animal and belittled for being the handicapped person he once was by the scientists. Emotionally in a turmoil, he decides to go back to New York.

Near the end of his journal account, Charlie explains why he is now going away from New York. At this point, he has run the gamut from being mentally handicapped to becoming highly intelligent to losing his intellect. The experiment that was supposed to permanently enhance his intelligence failed because the aging Dr. Nemur rushed it along: he wanted one last success to crown his long career.

The re-mentally handicapped Charlie confides to his journal that he made a mistake. He forgot he was no longer taking Miss Kinnian's class at the adult center, so he showed up for it. This so upset Miss Kinnian, who was once in love with him, that she started to cry and ran from the room. Charlie looked around and noticed that none of the other students were familiar. He realized he didn't belong in the class and had caused a scene:

Thats why 1m going away from New York for good. I dont want to do nothing like that agen. 1 dont want Miss Kinnian to feel sorry for me. Evry body feels sorry at the factery and I dont want that eather so 1m going someplace where nobody knows that Charlie Gordon was once a genus and now he cant even reed a book or rite good.

At least Charlie knows where he is in New York. The surroundings will be familiar, and he will feel a lot more secure in his environment. Back in Chicago, it was a whole different story. There, he felt like a carnival freak, a circus sideshow, patronized, lied to, and belittled by Dr. Strauss and Prof. Namur. They deliberately withheld vital information about Algernon's condition from Charlie, an indication that they regard him as little more than a lab rat or a guinea-pig, something to be experimented on. Despite his enormous intelligence, it's clear that Charlie will never get any respect from these men. They will always see him as an object of study, nothing more.

Overwhelmed by everything that's happened to him, and concerned that he'll end up the same way as Algernon, Charlie needs a change of scenery—and fast. As Charlie has little experience of the big wide world, he opts to return home to New York. There at least he stands a decent chance of finding his feet. Worried that his high intelligence won't last for much longer, Charlie most probably realizes that at least he'll have something to fall back on in New York, even if it just means going back to his old job at Donner's Bakery.

Charlie returns to New York because he is frustrated and little overwhelmed by the awarenesses and understandings effected by his increased intelligence.  As his IQ rises, he recovers lost memories from his childhood, and he finds that his growing relationship with Alice is adversely affected by his traumatic past.  Also, since he is now functioning at a genius level, he finds it is hard to communicate with other people. 

Charlie's view of Nemur and Strauss, the psychologist and neurologist who engineered the experiment that gave him his new intelligence, has changed as well.  He is insulted at being treated like an exhibition instead of a person, and is appalled at errors he now sees occurred in the handling of his operation.  Angry and disgusted, he retires to New York, where he lives a life of increasing isolation.