Each chapter of Chains opens with a date ranging from May 27, 1776, to January 19, 1777, and a quotation from a document of the time. Since the novel uses the voice of the protagonist, Isabel, it reads much like a diary. The story opens with the funeral of Mary Finch, slave owner of Isabel and her sister Ruth and former owner of their deceased mother. Mary’s nephew, Robert, sells Isabel and Ruth to a couple from New York City, the Locktons, devout Tories who scorn the American Revolution and the rebels fighting against the king. Throughout the novel, people loyal to Britain call those fighting for independence “rebels,” while the men and women fighting to be free from Britain’s rule call themselves “patriots.” 

Isabel and Ruth travel from Rhode Island to New York by boat. At the dock, Madam Lockton hits Isabel, the first of many blows. Ruth, age five, is simple-minded, so Madam keeps her near and dressed like a pretty toy, while she works Isabel hard. Isabel promised their Momma that she would always protect Ruth. Isabel meets and becomes friends with Curzon, slave to patriot Mr. Bellingham. Curzon proposes that Isabel work for the patriots by spying on the Locktons in exchange for her freedom since Isabel might overhear secret plans. Madam’s cruelty convinces Isabel to join the patriot cause.

Becky Berry, a white servant, and Lady Seymour, Mr. Lockton’s aunt, both show kindness toward Isabel and Ruth. Isabel learns that money hidden in the Locktons’ wooden crate will pay patriots to switch sides, information valuable to the patriot leaders. This scheme and the plot to assassinate George Washington lead to Lockton’s arrest, but Isabel’s role is not suspected. Each day, Isabel fetches water from the Tea Water Pump, a gathering place for slaves, and meets a kind Grandfather who gives her good advice. Grandfather often speaks of “crossing the River Jordan” as a metaphor symbolizing each slave’s path to personal freedom.

When Madam witnesses Ruth’s seizure, she immediately wants to sell her, and Isabel realizes that the list of conspirators in the library drawer could be their ticket to escape. Isabel goes straight to Colonel Regan in the patriot headquarters, who gives her the code for future visits. As the Tories’ plans are uncovered, Lockton flees the city, leaving his wife behind. Isabel and Ruth attend the public hanging of the man blamed for the assassination plot, and the British plant their navy in the harbor, preparing for war. The patriots officially declare their independence, and the city fills with soldiers.

Madam sells Ruth, or so she says, which so infuriates Isabel that she angrily confronts Madam, an act that incites injury and Isabel’s escape. Isabel runs to Colonel Regan, who cannot help her, and she is dragged to a dungeon. After three hellish days, a judge sentences Isabel to be branded with an “I” on her cheek for Insolence. The branding is so painful Isabel loses consciousness for days and wakes in Lady Seymour’s house, nursed back to health, fed, and cleaned, her cheek still burning. Isabel must return to Madam and spends the next weeks in deep sadness, ignoring Curzon and wishing ill on Colonel Regan.

Violent thunderstorms hit New York City. Curzon has joined the patriot soldiers, who lose the Battle of Brooklyn and retreat. When the British invade New York, Isabel decides to work for them instead, hoping she’ll earn her freedom this way. She reports the location of Washington’s headquarters to a British officer, hoping he will help her escape, but he cannot. Lockton returns, and the Tories celebrate victory. When the Locktons and Lady Seymour accept British and Hussein soldiers into their homes, Isabel goes to Lady Seymour’s to help her care for them.

When the Great Fire hits New York, Isabel helps Lady Seymour escape, but Lady Seymour suffers great injury and her home is destroyed, so she moves in with the Locktons, along with more British soldiers and their wives, who take over the household chores. The British capture Fort Washington and march the surviving rebels to the prison, including Curzon. As Madam holds a feast to celebrate, Isabel overhears more plans, including hopes that thousands of prisoners would starve or die of disease. As Isabel carries a bowl of food scraps to the yard, she devises a plan.

Isabel begins to visit the prison regularly, delivering food and checking on Curzon, who has been shot. She earns the trust of a guard and a patriot leader. She nurses Lady Seymour, who supports her helping the prisoners. A shop owner gives Isabel a copy of Common Sense. Isabel carries messages between the prison and patriot officers at a huge risk to herself.

On Christmas, Isabel takes a long walk near the waterfront. Madam discovers that she’s been visiting the prison and forbids her from continuing to do so, so Isabel decides she must act. That evening, Isabel bakes a bread pudding and gifts it to a family in the burned part of the city, keeping Christmas the way her Momma did. A few days later, when Captain Morse asks Isabel to deliver a message to the prisoners informing them that Washington defeated the British in Trenton, she hears the prisoners cheer with joy. Afraid for his safety, Lockton flees to England. Lady Seymour apologizes to Isabel for not protecting her more and buying her herself, but Isabel cannot forgive her. When the prison guard offers Isabel work cleaning out the cells, she wonders if it’s an opportunity to pay for her freedom.

The city plans a celebration of the queen’s birthday, including dancing, fireworks, and feasting. Lady Seymour has suffered a stroke, which has left her unable to move or speak. On the day of the ball, Captain Morse asks Isabel to deliver a coin to another officer. That officer gives Isabel a note for Captain Morse, which she puts in her pocket. At home, Madam is furious because someone told her that her slave, Isabel, is passing notes for the rebels. When Madam demands the note, Isabel tosses it into the fire, inciting Madam’s wrath. In her fury, Madam lets it slip that she still owns Ruth, who has been living in Charleston, and then she locks Isabel in the cellar. Soon, Isabel escapes, determined to find Ruth. She writes herself a pass in the library, naming herself Isabel Gardener. Lady Seymour lets her take coins to aid her flight and whispers, “Run!”

Isabel runs to the prison, claiming to be there to clean, and finds Curzon in very bad shape. She hides him in a wheelbarrow and wheels him outside. She practically carries him to the waterfront, where they must pass a group of British soldiers. As they do, fireworks from the queen’s ball light the sky and distract the soldiers. Isabel steals a boat and rows herself and Curzon to New Jersey with bleeding and frozen hands. She wakes on the other side, knowing that they are free.