After the operation, Charlie's intelligence rises slowly at first and then at a steadier, then eventually a very fast rate until he is an incredible genius.  Of course at this time he also realizes that he will soon be back in the state he was prior to the operation so he tries desperately to find a way to fix the flaws of the operation.

In the end, Charlie has returned to the level of intelligence he possessed at his birth.  He remembers, to some extent, that something was different but he does not remember any of the details and most of the memories fade completely after a while.  But the lasting effects are the ways that he has come to terms with who he is and those around him have done so as well, ending the story on a very successful note.