The Ship
The ship at the center of the novel is symbolic of humanity's last hope and last chance. After some kind of disaster (presumably man-made), humans are relegated to a "generational" ship capable of sustaining many generations of people on their way to a new homeland. Without the ship, humans would cease to exist as a species.
The Structure of the Ship
The structure of the ship (where dark-skinned people live on the bottom decks and where light-skinned people live on the upper decks) is symbolic of historical structural racism in the United States for much of its history. For much of the history of the U.S., darker-skinned people were segregated from lighter-skinned people and were the subject of racism.
The Sovereign
The Sovereign is symbolic of the privilege and racism of lighter-skinned people who live on the upper decks. The leader of the ship and the light-skinned people, the Sovereign is brutal, racist, and cruel, much like those who are racist in society.
The Experiences of Black People in the United States
The story of the novel is an allegory for the experiences of Black people in the United States during the Jim Crow era. Like the dark-skinned people on the ship, Black people in the United States were separated from white people. They were discriminated against and placed in different situations because of their dark skin.
Civil War
The civil war in the novel is symbolic of the pent-up anger and generational trauma many darker-skinned people have experienced throughout their time on the ship. For generations, darker-skinned people were abused and were treated in a racist way. One day, they finally had enough and started a civil war to reclaim their rights.