Flowers for Algernon tells the story of Charlie Gordon, a young man with a low IQ who has struggled since childhood with his lack of intelligence. Moreover, his mental retardation was the source of his mother, Rose's, consternation and, ultimately, frustration as she fought to "fix him." When she finally realized there was no hope in changing his condition, she actually threatened to end his life, as if it was worthless without the gift of intelligence.
After Charlie begins undergoing an operation that's intended to increase his intelligence, memories of his mother and her treatment of him begin to resurface. He recalls how she callously, and mercilessly punished, beat and chided him for not being like the other boys. Her resentment toward his mental state is essentially made more palpable as his mental acuity increases, and he struggles to come to terms with it.
The effect on Charlie as an adult is best realized in his affection toward Alice, a teacher at the Beekman College Center for Retarded Adults who at first insists they keep their relationship platonic. However, when they eventually do become romantic, Charlie finds himself unable to make love to her because he recalls his abusive mother physically attacking him for exhibiting even the smallest of sexual desires, a trauma that has stayed with him into adulthood.
Ironically, Charlie visits Rose at the height of his newfound intelligence in order to make peace with his past only to find that she has become demented and decrepit, a picture of deteriorated mental acuity who at first praises him for his achievements but later slips into delusion and attacks him with a knife. While a painful experience for him, it also has a cathartic effect since he now has the ability to recognize his own worth as a fully functional human being and Rose as the one who's irreparably flawed.