In his role as Secretary of State in the Adams administration, Marshall had failed to deliver commissions to 42 federal justices of the peace before the end of Adams's term. After coming to power, the Jefferson administration refused to deliver about half of these outstanding commissions, effectively preventing those individuals from receiving their appointments even though the Senate had confirmed their nominations. Though the position of justice of the peace was a relatively powerless and low-paying office, one individual whose commission was not delivered, William Marbury, decided to mount a legal challenge against the Jefferson administration. Seeking to have his judicial commission delivered, Marbury filed suit against the sitting Secretary of State, James Madison. The Supreme Court agreed to hear the case of Marbury v. Madison in its 1803 term. Meanwhile, the Democratic-Republicans passed the Judiciary Act of 1802, which effectively repealed the Midnight Judges Act and canceled the Supreme Court's 1802 term. They also began impeachment proceedings against federal judge John Pickering, a prominent Federalist; in response, Federalist members of Congress accused the Democratic-Republicans of trying to infringe on the independence of the federal judiciary.
Marbury v. Madison was the first case in which the Supreme Court struck down a federal law as unconstitutional and it is most significant for its role in establishing the Supreme Court's power of judicial review, or the power to invalidate laws as unconstitutional. As Marshall put it, "it is emphatically the province and duty of the judicial department to say what the law is." By asserting the power of judicial review in a holding that did not require the Jefferson administration to take action, the Court upheld its own powers without coming into direct conflict with a hostile executive branch that likely would not have complied with a court order. Historians mostly agree that the framers of the Constitution did plan for the Supreme Court to have some sort of judicial review, but Marshall made their goals operational. Though many Democratic-Republicans expected a constitutional crisis to arise after the Supreme Court asserted its power of judicial review, the Court upheld the repeal of the Midnight Judges Act in the 1803 case of Stuart v. Laird.
After his appointment to the Supreme Court, Marshall began working on a biography of George Washington. He did so at the request of his close friend, Associate Justice Bushrod Washington, who had inherited the papers of his uncle. Marshall's The Life of George Washington, the first biography about a U.S. president ever published, spanned five volumes and just under one thousand pages. The first two volumes, published in 1803, were poorly-received and seen by many as an attack on the Democratic-Republican Party. Nonetheless, historians have often praised the accuracy and well-reasoned judgments of Marshall's biography, while noting his frequent paraphrases of published sources such as William Gordon's 1801 history of the Revolution and the British Annual Register. After completing the revision to his biography of Washington, Marshall prepared an abridgment. In 1833 he wrote, "I have at length completed an abridgment of the Life of Washington for the use of schools. I have endeavored to compress it as much as possible. ... After striking out every thing which in my judgment could be properly excluded the volume will contain at least 400 pages." The Abridgment was not published until 1838, three years after Marshall died.