The allegory of Alice and Charles
When Alice and Fletcher are separated by their parents religious differences, she ends up forced to marry Charles, but then Charles and Alice die, leaving their kids to be raised by—you guessed it—Fletcher. This is a symbolic representation of the permanent nature of human love, and even though Alice and Fletcher were separated, they were still granted the fate they desired—to raise a family together. In other words, Fletcher was always supposed to raise Alice's children, so even when tragedy prevented it, their fate came about some other way. This is an allegorical reminder to not interfere with two people who are in love (and this is echoed at the end of the novel when Esther leaves Hope to marry Everell, arguing that they are destined to be together).
The war of Mononotto's vengeance
It was evil and wrong for the settlers to torture and murder Mononotto's son, but when he sees the gods blessing his honor killing of Everell, when he swings the blade to kill the innocent sacrifice, his plans are thwarted by his daughter (like the Greek tragedy Antigone). If Mononotto's religious opinions are valid and correct, then he has no choice but to admit that the gods have taught him a lesson about vengeance. The idea is perfectly clear: By holding grudges against those who harm us, we only further that harm. Peace was only available through forgiveness, as Magawisca urged her father to see.
Faith as a symbol for rejection
When Hope is chosen to stay with her father on his business trip to the ports on the New England coast, she is privileged above her sister, Faith, who is unaware of what it will mean to her. Her father's rejection literally leads to her abandonment of the culture and alignment with Native American culture, because his rejection led to her capture. And why did Fletcher prefer Hope to Faith? Because she was pretty like her mother. Faith's radical life is a representation of the chaos of her upbringing. She changes radically throughout the book because she doesn't have a stable community, having lost her parents and then ending up kidnapped because Fletcher was tired of looking at her, basically.
Hope as a symbol for peacemaking
Hope's role in the novel is the same as Magawisca's, but backwards. Magawisca argues with her leaders for mercy and understanding toward the foreign invaders. Hope does the same, but backwards, advocating for Nelema when she is tried for witchcraft, working with Magawisca to potentially end the war between them. Her name is important too, because with that, her character becomes symbolic. The symbol is that man's hope comes when we try to find peace in our differences, instead of exacting vengeance against one another for perceived injustices.
The paranoia motif
When something is going along nicely, and then it gets traumatically interrupted, that can cause a sense of paranoia. But in this novel, that happens all the time, and many of the characters are left in states of desperation and panic, because they always feel like they're about to get attacked. This makes them more willing to attack each other, and after a while, they're in a full-blown political war, because of one single injustice that could have been handled diplomatically. This novel explains that terroristic warfare leads to paranoia for all parties involved, because certainly, there will be retaliation.