John Adams' last three months in office were largely taken up with the reform of the federal judiciary. The country had soon outgrown the judicial structure created in 1789. That system provided for a Supreme Court of six justices, regional circuit courts, and district courts, with a Supreme Court justice required to preside over each session of a circuit court. The result was a nearly impossible schedule of travel for the justices, and one might be called upon to hear an appeal of a case he had helped to decide at a lower level. Frequent petitions from the justices had brought only minor relief, and it had become difficult to get able lawyers to accept appointment to the highest court.
In his annual messages of 1799 and 1800, the president had recommended judicial reform, but Congress proved unable to agree on a bill until after the results of the presidential election were known. Then the Judiciary Act of 1801 moved rapidly through Congress and was signed by Adams on 13 February. It reduced the Supreme Court from six to five at the next vacancy and created six new circuit courts presided over by sixteen new circuit judges, thus relieving the Supreme Court justices of circuit duty. A related act in the last week of February provided for an additional district court with three judges for the District of Columbia.
While Congress debated the Judiciary Act, Adams hurried to appoint a new chief justice of the Supreme Court. After serving on the peace mission, Chief Justice Ellsworth had remained in Europe to recover his health, and his resignation had reached the president in December. Unless a replacement could be confirmed before the Judiciary Act became law, there would be no vacancy and one of the associate justices would have to become chief justice. By appointing a Federalist and thus keeping the Court at six, Adams could make it unlikely that the incoming Republican president would be able to place a member of his own party on the bench for many years.
The favorite of many Federalists, Associate Justice William Paterson, was too close to Hamilton to please Adams. Instead, he nominated, and the Senate confirmed, John Jay, the first chief justice, who had left the Court to be governor of New York. Not in the best of health and regarding the judicial system as seriously "defective," Jay declined. It then dawned on Adams that his secretary of state, John Marshall, possessed the ideal qualities of age, diligence, and legal talent. He appointed Marshall on 20 January. The Senate delayed his confirmation a week while supporters of Paterson sought to change the president's mind. In February 1801 the chief justice whom history would acknowledge as the nation's greatest presided over his first session of the Supreme Court.
Altogether in the last ten weeks of his term, Adams appointed more than two hundred new judges, clerks, marshals, attorneys, and justices of the peace. He filled nearly all of these positions with Federalists of various shades, but most were moderate men of considerable ability. Thus he made one last great effort to put into practice his view of the presidency. On Tuesday evening, 3 March 1801, he signed the final three commissions. At four the next morning he left for Quincy, not waiting to witness the inauguration of Jefferson. Grieving over the recent death of his wayward son Charles and believing his duty finished, he headed into a retirement that would last until 4 July 1826, when both he and Jefferson died on the fiftieth anniversary of the independence of the nation in whose creation they had played such a major part.