Lee is, of course, referring to the loss of innocence in childhood, the knowledge that must come to all of us that there is evil in the world. She skillfully uses the physical setting in the chapter to convey images of darkness, and repeatedly uses "dark" words throughout the chapter. Here are some examples:
At the beginning of the chapter, we learn that is might be raining and, "There was no moon" (254). Shortly after, Scout says talks about "the solitary darkness" (254). Scout says they were "feeling their way" (255) and tells us they were far away from everyone. Scout reports that the lights in the distance were shining brightly, which makes the setting she and Jem are in seem even more dark. The word "dark" is used twice more on page 254.
When the children leave, they must walk out into the same darkness. Scout says, "We began crossing the black schooyard..." (259). She refers to Jem's outline being "barely visible" (260), and the word "dark" is used twice more on page 260, as well as other decriptions that show us the children can barely see.
After the attack, we get the contrasting image of light again, when "Light from our door framed Atticus..." (263). But in the house, as Jem is lying injured, his reading light has been covered with a towel, and "his room was dim" (265).
Lee's evocation of darkness, symbolizing the darkness of evil, which attacks the children in the dark, is beautifully rendered with setting, word choice, and contrast.