This may be a matter of opinion, because every teacher likes to focus on different aspects of a novel like this one. When I take a look with my students, I find the book to demonstrate innocence in several ways, but three in particular.
1. There is this storyline of Boo Radley throughout the book. From the beginning, the children find him to be the persona that the town believes: a phantom. The mystery of his character seems to turn out to be different than their original suspicions. In fact, he ends up being a hero.
2. The story of Tom Robinson's accusation and our experience of his innocence as facts are revealed throughout the trial and beyond seems to be a second major purpose of the novel.
3. Finally, the loss of the children's innocence as they discover the problem of humanity's judgement and Maycomb's prejudice occupies the majority of the book. This is important because these children seemed to live a life in which they can learn from the mistakes of the generation before them.
Your teacher may be looking for something different, but in short, this is one way to divide the book into 3 major happenings.