I read the short story version of Flowers for Algernon in eighth grade English and it has always stayed with me, so when I recently found out it was expanded into a novel I read it right away. So, herewith my thoughts on it, and as most people know how it all turns out there will be spoilers. :)
Charlie Gordon is a mentally handicapped man in his early thirties who has a deep-seated longing to learn to read and write, to be 'smart,' and through his classes at the Center for Retarded Adults in Brooklyn, he meets the teacher (Miss Kinnian) who will eventually nominate him for an experimental surgery at Beekman University. Dr. Nemur and Professor Strauss have succeeded (so far) in performing the surgery on a mouse named Algernon, which greatly raised the little guy's intelligence, and they feel ready to attempt the same on a mentally handicapped human being.
Probably the best thing about the story is that it is told through Charlie's own words, via progress reports he keeps for Nemur and Strauss. Through his basic vocabulary, misspellings, and complete lack of punctuation we are immediately drawn into his mind and his world, and it's heartrending to read. Like a child, he carries no natural suspicion of others, least of all his 'friends' at the bakery where he works as a janitor; he's superstitious, carrying a rabbit's foot and lucky penny; and he has no real memory of the past.
The surgery, as we might expect, is a success, and there's something really exciting in being able to follow along as his writing, via the progress reports, reflects his increasing IQ. We're right there with Charlie as he begins to really understand the world around him, and this of course inevitably means the good he formerly saw in people is exposed for what it is. For example, he believed the men who work at the bakery were his friends because they laughed at him, which in turn made him laugh and feel good; in reality, he was always only their foil, their court jester, and when Charlie realizes this, he is ashamed. (That was probably the strongest impression I took away from the short story, that moment when the veil fell away)
Eventually Charlie's intelligence far outstrips that of Miss Kinnian, Professor Strauss and Dr. Nemur; most people, in fact, as his IQ reaches 185 and beyond. He reads voraciously, teaches himself twenty languages, becomes an expert on fringe mathematics – the world of thought is his oyster. At the same time, Algernon (who had the surgery weeks before Charlie) begins a slow decline.