In Flowers for Algernon, Charlie and Algernon are both connected. Algernon was the first to "become smart," and Charlie followed. The reader knows from the beginning that their fates are intertwined; what happens to Algernon happens, at some point, to Charlie.
Algernon and Charlie both had their intelligence increased, and both became abnormally intelligent. Algernon and Charlie enjoy a bond that is both a deep connection and a symbolic relationship. In a literary sense, Algernon symbolizes Charlie.
As Charlie becomes smarter, he sees the connection as well. He understands that Algernon's behavior foreshadows his own fate. Therefore, when Algernon's behavior alters, Charlie knows that it is more than likely to happen to him as well. Thankfully, Charlie is so smart at this point that he is in a position to try and delay any changes from happening to himself. That's why he begins to work so intensely. With his great mind, Charlie is attempting to find any way he can to stop the changes from occurring within his own mind.
Sadly, of course, Charlie learns that it is not possible. His great intelligence could not save him from his fate, a fate that mirrors that of Algernon. Both were allowed only a brief moment of glory, despite the best efforts of those who tried to make this brief moment last.
Well, it represents their key of achieving their long term dreams. It can also symbolize Walters greed and the destruction to his own original beliefs.
