The initiating event was when Charlie did the inkblot test and couldn't see anything in the inkblot.
Charlie realizes that he has been treated cruelly by his "friends" at the bakery, and the people around him.
Charlie leaves his job at the bakery. He feels alienated from the people around him, including Alice.
Charlie is taken to a scientific convention in Chicago. They show pictures of him in early interviews, which he wasn't aware of. He takes off with Algernon back to New York and soon realizes he doesn't have a lot of time left.
Charlie and Algernon return to the lab and Algernon dies.
Charlie's grammar, spelling, coordination, and regression bgin to get worse. His final wish as he finishes his last progress report is for someone to put flowers on Algernon's grave.