There are many examples of both internal and external conflict in Daniel Keyes's "Flowers for Algernon," but I will focus on the struggle between Charlie Gordon and his intelligence, which is the central conflict in the story.

Charlie has special needs and longs to be smarter. The framework for "Flowers for Algernon" is a series of progress reports written by Charlie, who undergoes an experimental surgery to increase his intelligence. Throughout the course of the story, we see a drastic change in his reports. Prior to the surgery, his spelling, grammar, punctuation, and understanding of his surroundings and the world are limited. After the surgery, we see gradual improvements in his spelling, grammar, and punctuation, as well as a heightened sense of awareness and a clearer understanding of the world and the people in it.

Charlie becomes increasingly more intelligent after his operation. Although his goal is realized, this intelligence presents a new set of conflicts, which complicate his life. Prior to his surgery, Charlie is unhappy, because he wants to be smart. His lack of intelligence is a source of discontentment, however, as his ignorance prevents him from being aware of the cruelty of the people around him. He does not realize that his coworkers are laughing at his expense; he believes they like him and are his friends. He does not realize that his doctors are taking advantage of him by allowing him to participate in an experimental surgery, even though he does not have the mental capacity to give informed consent. After his surgery, Charlie realizes that the people he thought were his friends were making fun of him all along. He is fired from the job he loved because his coworkers are uncomfortable with his newfound intelligence. He now understands his doctors' corrupt motivations: "When I left afterwards, I found myself trembling. I don't know why for sure, but it was as if I'd seen both men clearly for the first time."

The effects of the experimental surgery are short-lived, and Charlie's intellectual capacity declines. Aware of his regression, he becomes depressed and distances himself from others, including his teacher and love interest, Miss Kinnian. As the effects of the surgery wear off, we see Charlie's writing gradually revert back to the way it was before his operation. His spelling, grammar, and punctuation become increasingly poor. He struggles to understand his loss of intelligence and blames himself for his devolution: "I dont know why Im dumb agen or what I did wrong maybe its because I didnt try hard enuff."

The central conflict in the story is the internal struggle between Charlie and his intelligence. Prior to the surgery, Charlie is dissatisfied and longs to be smart. After the surgery, he sees the world with new eyes, and along with his increased intelligence comes a new set of conflicts and complications resulting from a clearer understanding of the world. When the effects of the operation wear off, Charlie blames himself and struggles to understand the loss of his intellect.

The main conflict in Flowers for Algernon is an internal one, that between Charlie and himself. Throughout his whole life, Charlie has struggled hard to overcome his acute learning disability. In practical terms, this has involved his taking classes at a local college in order to improve his intelligence.

Simply put, Charlie's not happy with himself and wants to do so much better in life. Tired of being thought of as stupid and sick of only being able to hold down menial jobs, he's desperate to overcome his intellectual limitations and effectively become a different person.

To a considerable extent, Charlie's inner conflict arises from a difficult childhood, when he was subject to emotional abuse by his mother. In trying to escaping from the consequences of his learning disabilities, Charlie is also endeavoring to put his abusive childhood behind him. Though no longer a child, Charlie still finds himself tormented by his childhood, against which he's engaged in an almost constant struggle.

One gets the impression that Charlie will never fully escape the traumas of the past unless and until he can become the intelligent young man he so desperately wants to be. But for the time being, the struggle between Charlie and himself will continue.

Much of the conflict in Flowers for Algernon is an internal one. Charlie struggles with the decision to have experimental intelligence-enhancing surgery. Before the surgery, Charlie is generally content with his life. Despite the abuse he receives at the hands of people he considers to be his friends, Charlie always tries to be kind to others. He is always trying to improve himself. That is why he attends night school and endeavors to learn to read and write. This is difficult for him due to his problems remembering just about everything. When Charlie learns about the experimental surgery, he is conflicted as to whether or not to proceed. He keeps himself busy in the days before the surgery in order to stay distracted. He is ultimately encouraged to proceed by his teacher Alice Kinnian and Algernon, a mouse that has already undergone the procedure.

The conflict continues after the surgery as Charlie reckons with his new understanding of the world. He redoubles his efforts to learn, this time with greater success than ever before. However, his "friends" at the bakery still treat him poorly. Charlie struggles with his relationship with them. He learns that one of them, Gimpy, is stealing from the bakery. Charlie is conflicted about what to do. Confronting Gimpy just makes things worse. He also begins to recall more terrible memories from his childhood. Furthermore, Charlie begins to resent the scientists who see him as more of a science fair project than an actual person. All this new intelligence is making Charlie more jaded with the world than he ever was. All this points to the central conflict of how to deal with the sudden onset of intelligence after a life of semi-ignorant bliss.

A conflict in literature is a struggle between forces that oppose each other. In "Flowers for Algernon" the essential struggle occurs between Charlie's desire to be intelligent and a natural order or fate that has decided he must be mentally handicapped.

From the start of the story, Charlie is struggling to better himself. He knows he is not as smart as other people and has a strong desire to change this situation. He therefore attends night school and in that way, through his teacher Miss Kinnian, he comes to the attention of two scientists who believe they can increase his intelligence through an operation.

Charlie agrees to the operation and, for a time, it seems all his dreams have come true. He becomes highly intelligent. Then it becomes clear that the operation is a failure, and he will backslide to his old condition. He is back in conflict with the force of nature—his genetic makeup—which has decreed he must be mentally deficient. It is the sad story of a person who cannot be who he wants to be.

In answering this question, it is important to note that "Flowers for Algernon" started as a short story and was later turned into a novel.  naturally, the subsequent novel had more complex conflicts than the short story.

However, the central conflict in both versions of the story center on Charlie's changed life as his intelligence grows, both in his interaction with his co-workers and his growing love for his teacher.  Furthermore, the state of degeneration that his mental growth has on Algernon is a horrible conflict that goes on within Charlie.  Ultimately, Charlie's changing his mind is insufficient to save Algernon's life.