Scout explains the plot of "The Grey Ghost" as Atticus puts her to bed: A gang of boys accuse Stoner's Boy of destroying their fort, but “'[w]hen they finally saw him, why he hadn't done any of those things . . . Atticus, he was real nice. . . .'” Atticus's response to this is “'Most people are, Scout, when you finally see them.'”
This directly relates to Boo Radley; the kids (and the town) thought Boo was a terrible monster, but, when Scout got to know him, she saw that he was a nice guy and saved her life. Atticus teaches her his final lesson of the book with his statement.
The reader first learns about The Gray Ghost in chapter one when Dill bets his copy against two copies of Tom Swift that Jem "wouldn't get farther than the Radley gate" (13). In chapter 31, Atticus finds the book (obviously won by Jem) and reads it to Scout to put her to sleep after being assaulted by Bob Ewell on Halloween night of her third grade year. The basic plot of The Gray Ghost revolves around someone called "Three-Fingered Fred 'n' Stoner's Boy" (280). Everyone in the book thinks that Stoner's Boy ruined their clubhouse when they find ink all over it. Most of the story is about them trying to find Stoner's Boy because they don't even know what he looks like. (This creates mystery and suspense that Scout also says is scary. In fact, she says that life isn't scary but books like The Gray Ghost are.) When they do finally find Stoner's boy, though, they discover that he wasn't the one who dumped ink all over their clubhouse, and they find out that they had wrongly assumed the worst about him all along. Scout says that "when they finally saw him, why he hadn't done any of those things . . . Atticus he was real nice" (281).
Atticus verifies that this is the case with most people throughout life. If we just took more time to get to know people—to really see them—we would discover that they really are nice and not anything like what rumors or assumptions might lead others to believe. And, as stated in the other answer, The Gray Ghost does create a parallel reference to Boo Radley. At the end of To Kill a Mockingbird, the kids know for sure that Boo isn't one to peek into their rooms or do any of the other horrifying things Miss Stephanie Crawford says he does around town at night.