Amir simply watched his best friend, Hassan getting raped by 3 other boys in the alley. After the incident, Amir acted ignorant and pretended he didn't see what happened. He reacted the opposite of what he should've and became angry with Hassan. Amir was frustrated with Hassan for being too loyal and not being angry with Amir. I think both the boys know that Amir saw what happened. Because of this, Amir feels a big sense of guilt but decides not to do anything about it. However, in the "present" part of the book, he wants to go back and make things right with Hassan.
I'm not sure what to say about the whole concept of atonement because in some cases, I think past mistakes can be forgiven and made "right" but there are others that can't be. I think everyone deserves a second chance at things but I don't know if that fits the definition of "atonement".