Big spoiler alert ahead, Shmoopers, and it's a tear-jerker: Charlie is finally back to square one, and then some; his intelligence has regressed to the point where he can barely take care of himself. And to make matters worse, the poor guy goes back to Miss Kinnian's classroom just like he used to do. When Miss Kinnian cries and runs out of the room, Charlie gets the sense that he's really in the wrong place. He's "pulled a Charlie Gordon" (309), if you will.
So he pens a final letter to his loyal friends and former colleagues, letting them know that he's checking himself into the Warren Home school. If they'd only be so kind to "put some flowrs on Algernons grave in the bak yard" (311), he can finally rest easy. Tear.
We knew from midway through the book that Charlie was going to lose his smarts, but it still comes as a shock to the system when it actually happens. Without his big brain, Charlie gets the idea that he's not welcome in society. People will either laugh at him or feel uncomfortable, and how's that for a life? Charlie, we don't think you need to do the changing.
Here's what Charlie does want: people to recall him fondly and often. If his old friends will just put flowers on Algernon's grave, there's a chance they might remember lessons learned from Charlie's experience too.