What do you think becomes of Charlie after the story ends in Flowers for Algernon?
Prior to becoming a subject of an experiment, Charlie works in a factory and he is often the victim of teasing and bullying. Other workers take joy in setting Charlie up. After Charlie loses his intelligence, those very workers began to defend Charlie. This is probably the only positive change in the story. If Charlie were to stay with the factory, he probably would have a better experience working there.
Another possibility is that the experiment may have damaged Charlie such that his life would be shortened. After all, the mouse Algernon died following his loss of intelligence.
In any case, Charlie has been abandoned by the researchers and has lost the abilities he cherished. He has lost his teacher. He is significantly worse off than prior to the experiment and his remaining life would probably reflect these facts.
In the book Flowers for Algernon, Charlie has always been an intellectually impaired person. He was provided with the opportunity to experience a higher intelligence quota, but once he lost it, he returned to his former self. Because Charlie will no longer have the higher level of cognitive skills, he will return to menial labor jobs.
The situation with Charlie is complicated when he returns to his former intelligence. Because of the experiment, he had gained the ability to learn and understand things that had been beyond his comprehension prior to the experiment. Charlie had experienced what it was like to function with a higher level of intelligence.
Charlie may experience feelings of loss and depression when he thinks back on the interactions he had with others and the hopes he had when he was no longer cognitively impaired. Many people with cognitive impairments understand the limitations that their disability causes. Because Charlie had a chance to feel what it was like not to be impaired, he may become more easily frustrated. In Charlie's case, he may have been better off never having had the experience of higher intelligence because returning to his former life may be a let down.