The reader often encounters the motif of flashbacks throughout Flowers for Algernon to reveal the roots of Charlie’s trauma and his awful family history. Charlie’s flashbacks to his past begin after the operation and occur more and more frequently until his mental state has almost fully declined. Each one gives the reader insight into key moments that help explain the shame and fear Charlie carries as an adult. Through these flashbacks, the narrative shows abuse from Charlie’s mother, neglect from his father, and endless moments where Charlie’s intellectual disability is a horrible source of humiliation for him.
In the days before the experiment that changes his brain, Charlie doesn’t have any flashbacks because his low intelligence and limited self-awareness prevent him from recalling detailed memories. Before the surgery, he does not have the cognitive ability to reflect on his past, so he doesn’t understand how his earlier experiences have affected him. The experiment increases his intelligence and self-understanding. This allows him to interpret and revisit memories in vivid detail, which he finds frightening at first. The flashbacks grow more frequent as Charlie’s intelligence rises, and he begins to feel angry and resentful about how others treated him when he was unable to understand their actions. Stress or strong emotions often cause these memories to resurface for Charlie. As his mind becomes sharper, he sees the choices of his family and “friends” in a new, less rosy light.
Keyes uses these returning memories not only to fill in Charlie’s personal history for the reader, but also to show the impact of repeated abuse. Each flashback draws a direct line from Charlie’s past to the present. Cumulatively, they explain why he reacts to certain situations with fear or confusion. The repeated motif of flashbacks makes the reader aware of how Charlie’s trauma lives on no matter how much Charlie changes. The novel uses this technique to show that intelligence alone cannot erase—or repair—old pain. Although it benefits Charlie to be able to recall his past, the new understanding he gains doesn't make him any happier than his ignorance did.
Keyes develops a recurring motif of abandonment and isolation in Flowers for Algernon, which shapes Charlie’s experience from the start of the novel to the end. Charlie begins the story alone aside from his teacher Alice and his so-called “friends” at work. He hopes that intelligence will help him form real connections and be less lonely. For a brief time after the surgery, he does connect with other people.
However, as his intelligence grows, the distance between him and others also grows. By the time he reaches his most advanced state, Charlie feels cut off from everyone. Just like when his IQ was low, he is unable to share his thoughts or feelings fully because he cannot put them into words others will understand. When his intelligence quickly declines, he returns to the same isolation he faced before the operation. Despite everything, he ends the story as alone as he began.
Throughout the novel—although the reasons for it change—Charlie faces exclusion at every turn. Before the operation, people leave him out of things or mock him because of his low intelligence and extreme gullibility. After the surgery, the same people pull away for a different reason. Now that he’s smart, they cannot understand him, and many of them feel threatened by his new abilities or disgusted by his newfound pride and arrogance. There’s no period of Charlie’s life, in other words, that gives him lasting happiness or acceptance. Each change in intelligence only brings on a new form of separation.
Keyes also uses Algernon’s trajectory to reinforce this motif. Algernon lives alone in his maze, always racing against himself. He never shares his experiences with others despite how extraordinary they are, and eventually he dies in isolation. Algernon’s existence in the maze has a series of goals that he must achieve despite limited choices, just like Charlie. The repeated pattern of being left alone (no matter how one changes) is a big part of why this novel is so overwhelmingly sad.