In this scene, Bod comes to the graveyard for the first time and meets his future parents, Mr. and Mrs. Owens. At first, the ghosts were hesitant about letting him stay, but the Lady on the Grey told them to "have charity."
In this scene, Bod was upset that Silas had to leave and that Mrs. Lupescu was taking Silas' place as Bod's teacher. At first, he didn't like her, and they didn't get along. Eventually, he realized that she was teaching him important things, and they both grew to understand each other.
In this final scene, both Bod and Silas are leaving the graveyard permanently. Bod feels sad and will miss everyone, but he realizes that it's important that he leave his childhood home and grow and live elsewhere.