An allegory can be defined as a "figure of speech in which abstract ideas and principles are described in terms of characters, figures ad events" ("Allegory"). Daniel Key's short story "Flowers of Algernon" is an allegorical science fiction story aimed at criticizing the actions of science. Specifically, it points out that the mentally retarded protagonist Charlie Gordon was treated like an animal, just like the lab mouse Algernon, in the name of scientific advancement. However, the ultimate end result is death for Algernon and a great deal of heartache and disappointment for Charlie.
One allegorical detail we can find in the story is the fact that in his journal, Charlie misspells the Beekman School for Retarded Adults that he attends as the "Beekman School for retailed adults." This one small slip of Charlie's pen actually has great significance. Charlie is indeed being treated as an adult who can be "retailed." Once the scientists feel their experiment on Charlie has been successful, they put him up for display at the annual psychological association convention in Chicago so that the science can literally be sold to other scientists.
A second allegorical detail can be seen in the maze Charlie is asked to complete early on in the story. The maze, which Charlie calls "amazed" is labeled "START and a FINISH" and allegorically symbolizes the entire journey the scientists have Charlie complete. Charlie starts out being a retarded adult and treated like he is sub-human, becomes amazed by his own abilities to be smart, and then finishes off right back where he stared, in an institution, showing us just how wrong it was for the scientists to think of him as sub-human and put him on such a terrible journey in the name of science.