The primary conflict of the story concerns Atticus's defense of Tom Robinson, who is falsely accused of assaulting and raping Mayella Ewell. Given the fact that Tom Robinson is a black man, there is a significant amount of controversy surrounding the upcoming trial. As a naive child, Scout struggles to comprehend the specific details of the case but tries her best to understand why Tom Robinson is in trouble.

In chapter 12, Cal takes Jem and Scout to Sunday service at First Purchase African M.E. Church and Scout watches as they take up a collection for Helen Robinson. When Scout asks Cal why Helen cannot get a job, Cal explains that Helen's husband has been accused of raping Bob Ewell's daughter. When Scout asks Cal what rape is, Cal carefully avoids the question by saying,

It's somethin' you'll have to ask Mr. Finch about ... He can explain it better than I can.

In chapter 14, Scout remembers to ask her father the definition of rape. Atticus recognizes that Scout is too young to be told the explicit definition but tells her

rape [is] carnal knowledge of a female by force and without consent.

Atticus's definition of rape goes over Scout's head but seems to satisfy her curiosity.

In addition to being brought up in chapters 12 and 14, rape is also discussed during the Tom Robinson trial in chapters 17 and 18. Bob Ewell testifies that he saw Tom Robinson "ruttin’ on my Mayella!" and Mayella also falsely accuses Tom of raping her. When Bob Ewell testifies that he witnessed Tom Robinson raping his daughter, Reverend Sykes asks Jem to remove Scout from the courtroom because she is too young to listen to the explicit details of the case. There is no indication that Scout fully comprehends the nature of Tom's alleged crime but she does recognize that he is the tragic victim of racial injustice.