In the story, Moose is charged with taking Natalie with him wherever he goes. While he loves his sister, Moose privately resents this new state of affairs; faced with a responsibility beyond his years, Moose has to reconcile his growing sense of discontentment with his desire to please his parents. This is an example of internal conflict in the novel, where a character (Moose) must struggle with conflicting feelings. In this case, Moose's mother has charged Moose with the very adult job of tending to Natalie after school hours.
Not only is Moose responsible for Natalie's safety, but he must also ensure that Natalie is as involved as possible in everything he does. This is a tall order, and things eventually come to a head when Moose finds Natalie sitting with Convict 105. Although Natalie seems happy, Moose is terrified that something could have happened to her while his back was turned. He remembers the warden's initial words when his family first came to Alcatraz: "Some of these convicts haven’t seen a woman in ten or fifteen years. I think you’re old enough to understand what that means..."
This incident with Natalie and convict No. 105 is the catalyst for Moose's emotional conversation with his mother later. In Moose's mind, the responsibility he has is beyond his years and experience. As a rule, he feels resentful and guilty much of the time. In one conversation with his father, Moose asks whether he is responsible for Natalie being the way she is. Distressed at the pressure his son is under, Mr. Flanagan assures Moose that he is in no way responsible for his sister's condition. Yet, Moose knows in his heart that his parents are making Natalie's condition worse by ignoring certain truths about her.
First, Natalie is sixteen, but her parents treat her as if she is ten. Moose's mother especially expects him to play along, so that Natalie will have a chance to attend the prestigious Esther P. Marinoff school. However, as time progresses, Moose finds it more and more difficult to ignore Natalie's emerging maturity. He also finds it increasingly difficult to keep her safe. This is why he often vacillates between guilt, anger, and love.
The internal conflict within Moose is resolved when he comes to the conclusion that he is not wrong for wanting Natalie to be treated as a sixteen-year-old girl (which she is). He tells his mother that all of them have to stop pretending that Natalie is ten. It is only when Moose is able to reconcile his conflicting feelings that he manages to help his mother understand the depth of his love for Natalie and to change her perspective regarding Natalie's care.