The story begins on July 2, 1773, in the Boston, Massachusetts silversmith shop of elderly Ephraim Lapham, where protagonist Johnny Tremain is a promising 14-year-old apprentice. It is understood that some day he will marry Mr. Lapham's granddaughter Cilla to keep the shop within the Lapham family. The shop soon receives a challenging and urgent order from wealthy merchant John Hancock to make a silver dish to replace one that Mr. Lapham fashioned decades before. While preparing Hancock's order, Johnny's hand is badly burned when Dove, an older apprentice resentful of Johnny, deliberately gives him a cracked crucible that leaks molten silver. Johnny's hand is crippled beyond use, and he can no longer be a silversmith. Johnny's youthful pride is crushed by the injury, which has made him useful only as an unskilled errand boy.
After a series of rejections, Johnny reaches the low point of his young life. He turns to Mr. Lyte, a wealthy Boston merchant. Johnny explains that his mother told him that he and Mr. Lyte are related and as a last resort, to turn to him for help. Lyte requests proof, and Johnny shows him a silver cup with the Lyte family's crest. Lyte says it was stolen from him in a burglary and Johnny is arrested. Eventually, Johnny is freed by the court after Cilla testifies that he showed her his cup before the burglary ever took place.
Johnny settles into a job delivering a weekly newspaper, the Boston Observer. The Observer is a Whig publication, and Johnny is introduced to the larger world of pre-revolutionary Boston politics by his new friend and mentor Rab Silsbee, an older boy working for the paper. Johnny learns to ride and care for Goblin, a beautiful but skittish horse used to make deliveries, and moves in with Rab in the attic of the newspaper's shop.
As months go by and tension between Whigs and Tories rises, Johnny becomes a dedicated Whig himself. Johnny matures and re-evaluates many personal relationships, including that with Cilla, who becomes a trusted friend and fellow Whig. Johnny and Rab take part in the Boston Tea Party, in which Boston patriots throw a shipload of tea into Boston harbor rather than allow the ship's owner to unload the tea and pay a tax imposed by Parliament in London without the consent of the people of Britain's American colonies. In retaliation Britain sends an army to occupy Boston and closes Boston's port, inflicting hardship upon the inhabitants of this commercial and trading town.
Johnny acts as a spy for the Sons of Liberty, a secret organization of Boston Whigs fomenting resistance to Britain, when in addition to his newspaper deliveries, he is paid by British officers to carry their letters to outlying towns. He becomes a trusted member working with prominent Whig leaders John Hancock, Samuel Adams, Paul Revere and Doctor Joseph Warren. Rab is also a member and drills with the Minute Men at Lexington, but he frets at not having a modern musket with which to fight. Johnny, unable to fight because of his hand, obtains a musket for Rab by helping a British soldier to desert. However he is badly disturbed when the deserter is caught and executed.
The novel reaches its climax in April 1775 with the outbreak and immediate aftermath of the Battles of Lexington and Concord. Prior to the battle the leading Whig leaders convene in the attic where Johnny and Rab sleep. James Otis, once an active member but recently shunned by the group due to his recurrent bouts of insanity, comes to the meeting uninvited. Otis, quite sane on this night, stands hunched under the sloped beams of the Observer's attic and explains to those present what the impending fight with the British is really about: "We give all we have . . . even life itself--only that a man can stand up." Although the beginning of the war has brought about the death of Rab, the scorned American militia have defeated the powerful British army in their first battle. Johnny submits to an operation by Doctor Warren that will repair his hand and allow him to take up Rab's musket.