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One might be the injustices perpetrated by the upper class; Sir Philip takes the land away from the people and threatens anyone who goes against him.
Another might be the role of women, as seen in the character of Kit who is actually a girl disguised as a boy to avoid having to marry Sir Philip. She does not love him, nor does he love her; he is only, as the rich often are, interested in her inheritance. Loyalty to one's monarch might be a third main idea, since Kit and Peter help put down a rebellion by reporting it to the Queen and stopping those who would align themselves with Spain against the Queen