The physical confrontation sets up a crucial theme in the novel: Evil hides in the dark, trying to kill that which is good. Bob Ewell has told Atticus that he would seek revenge against him for defending Tom Robinson in the trial, but Atticus likely didn't foresee that Bob would seek out his children. In the dark, Bob has attacked Jem and Scout with every intention of killing them. Jem has been more badly injured, and Scout is scared at first that he has died. Bob Ewell personifies evil: he has no redeeming qualities in the story and only seeks to destroy goodness.
Another theme that emerges is this: When times are tough, ordinary people can do extraordinary things. Boo Radley has lived as a recluse in his house for many years. It is clear through this scene that he has still been keeping an eye on the children who played games in and near his yard, and he knew they were in danger on this night. Boo hides himself in the woods and emerges just in time to save the kids from the danger of Bob Ewell. Boo kills Bob and takes Jem home to Atticus. After this heroic act, he doesn't emerge from his house again. His extraordinary bravery saves the kids's lives.