After he finds out that he's going to lose his intelligence, Charlie goes to visit his mother before it happens. Suffering from dementia, she doesn't recognize him first, but when she does, she's proud of him. For the first time in his life, Charlie feels accepted by her. He also meets his sister, Norma and sees that she became a kind and caring woman, unlike the Spoiled Brat he remembered.
Near the end, when Charlie's intelligence is on the decline, and he goes back to the box factory. Specifically, when one of his coworkers (who was hired after Charlie had quit) started making fun of him in a manner resembling his treatment at the start... then Joe Carp stepped in, gripped the guy's shirt, and told him that if he did it again, he'd break his scrawny neck.
When Charlie's journal entry asks that someone else put flowers on Algernon's grave after he's no longer able to — hence the title.
When Charlie returns to the bakery after reverting back to his former self, the same people who made fun of him and hated him when he got smart stand up for him when a new worker bullies him.
In the novel, Charlie still feels bad because the new worker has a wife and child to support, and he thinks that the new worker shouldn't have to get fired just for bullying him.