At the beginning of chapter 12, Scout records that Jem begins breaking away from her and changing:

This change in Jem had come about in a matter of weeks. Mrs. Dubose was not cold in her grave—Jem had seemed grateful enough for my company when he went to read to her. Overnight, it seemed, Jem had acquired an alien set of values and was trying to impose them on me: several times he went so far as to tell me what to do.

Jem is entering adolescence, a difficult period for him. He starts feeling much older and wiser than Scout and takes it upon himself to order her around as her superior. This, of course, does not go down well with Scout, who says,

In addition to Jem’s newly developed characteristics, he had acquired a maddening air of wisdom.

Calpurnia advises Scout that Jem is growing up and tells her to give him time and space to be by himself so that he can work out his issues. She tells Scout to come to her in the kitchen if she is feeling lonely.

When Scout asks Atticus if she has to mind Jem when he bosses her around, Atticus says only if he can make her. Atticus knows that Scout is not likely to put up with Jem lording over her—and she does not. However, she is hurt when she wants to talk to him about the hypocrisy of her teacher for condemning Hitler's treatment of the Jews while condoning the racial prejudice in Maycomb, and Jem just shakes her and yells that he doesn't want to hear her talk again about the Robinson trial. Scout is so upset about this that she seeks out Atticus, who says,

Don’t let Jem get you down. He’s having a rough time these days.