In Chapter 6, Jem and Dill decide to take their pursuit of getting a glimpse of Boo Radley to a new level: They cut through the Radley's back yard and peek in a rear window of the house in the hope of seeing the "malevolent phantom" who lives inside. Scout only decides to come after Jem accuses her of "gettin' more like a girl every day." But when Jem tries to look inside, Scout then
... saw the shadow. It was the shadow of a man with a hat on...
The shadow stopped about a foot beyond Jem. Its arm came out from its side, dropped, and was still...
Jem leaped off the porch and galloped toward us. (Chapter 6)
As the children race to safety, a shotgun blast is heard, and Jem becomes entangled on the wire fence that surrounds the Radleys' collard patch. Unable to free himself, Jem slips out of his pants and leaves them behind.
After suffering the indignity of being discovered in his underwear by the gathered neighbors, Jem decides to return later that night to retrieve his lost pants. But when he returns, he finds them
"... folded across the fence... like they were expectin' me.
"And something else-- ... They'd been sewed up. Not like a lady sewed 'em, like somethin' I'd try to do. All crooked. It's almost like--"
"--somebody knew you were comin' back for them." (Chapter 7)
Although we find out much later in the novel that Atticus eventually learns about the children's excursion, there is really no one else who could have mended Jem's pants but Boo. It is certainly not Boo's brother, Nathan, who fires the shotgun as a warning to the prowlers. The folded breeches is just another instance of Boo keeping an eye out for his young neighbors, just as he does on the fateful Halloween at the end of the story.
Jem reveals that his pants were mended and folded over a gate. Jem suspects that Boo is responsible.