Who is Charlotte Doyle? That's the question this novel asks us not once, not twice, but like about a billion different times. Is Charlotte her father's daughter? Is she Zachariah's friend? Is she just her own sassy self? Identity, you see, can be constructed in many different ways. Sometimes Charlotte sees herself in relation to someone else (for example, the Captain), and at other times as part of a group (like when she joins the crew). There are even moments when Charlotte imagines herself to be completely autonomous (that means that she's an individual who acts all on her own). Which forms of identity do you think the novel portrays most positively? More importantly, how do you identify yourself?
Charlotte must learn to be completely independent. Only then can she figure out who she really is.
Charlotte finds out who she is by connecting with different people and joining new social groups. It's the choices that she makes that matter.