Although Atticus presents a defense that gives a more plausible interpretation of the evidence—that Mayella was attacked by her father, Bob Ewell—Tom is convicted. He is later killed while trying to escape custody.
After the verdict is announced, while he is not surprised, Atticus is very bitter. He knows the people of this town are changing, but they were wrong to have just killed an innocent man due to their racist ways. Atticus simply tells Jem that it's not right, and continues on like nothing happened.