For the first two months covered by this volume, Thomas Jefferson is residing at Monticello, avoiding the "rather sickly" season in the nation's capital. His mountaintop house finally has a roof and both daughters and their families come to stay with him. Using cowpox vaccine received from Benjamin Waterhouse, he undertakes what he calls "my experiment," the systematic inoculation of family members and slaves against the smallpox. In Washington, the construction of buildings for the nation's capital moves forward. The walls of the chamber of the House of Representatives now extend "up to the window heads," with only three feet more to go. Jefferson considers the erection of this chamber as well as completion of a "good gravel road" along Rock Creek as crucial for "ensuring the destinies of the city." The interior decoration of the President's House also progresses, with draperies, girandoles, and a chandelier furnishing the circular room. His carriage is ready to be shipped from Philadelphia. As the city takes shape, so too do the operating principles of Jefferson's administration. He dispatches a letter to his heads of department outlining "the mode & degrees of communication" for conducting their business. In mid-November, he enters a period of intense activity in the preparation of his first annual message to Congress, soliciting suggestions but personally drafting the document that he will submit in writing in early December.

The period covered by this volume brings to a conclusion Thomas Jefferson's first year as president. On 8 December he communicates his first annual message to Congress: peace between France and England is restored; a rise in population will increase revenue and help abolish internal taxes; the standing army can be done away with; "peace & friendship" prevail with Indian neighbors. He recommends two particular matters to the attention of Congress: a revision of the laws on naturalization and a review of the Judiciary Act. Two delegations of Indian nations hold conferences with Jefferson and Secretary of War Henry Dearborn in Washington. Jefferson observes that it is good for them to "renew the chain of affection." The president receives a "Mammoth Cheese" as a token of esteem from the citizens of Cheshire, Massachusetts, and the letter from the Danbury Baptists arrives. In his famous reply to the Baptists, Jefferson states that "religion is a matter which lies solely between man & his god." Shortly after legislators arrive in town for the opening of Congress, he begins to entertain at the President's House. He uses such occasions to bridge the divide between the executive and legislative branches and foster political understanding between Republicans and Federalists. As he moves into his second year as president, he is optimistic about his legislative program and the Republican majority in Congress.

This volume opens on 13 November 1802, when Jefferson is in Washington, and closes on 3 March 1803, the final day of his second year as president. The central issue of these months is the closing of the right of deposit at New Orleans, an act that threatens the economic wellbeing of Westerners. Jefferson asks his old friend Pierre Samuel du Pont de Nemours to remind the French government of the strong friendship between the two nations. To disarm the political opposition, the president sends James Monroe, who is respected by the Federalists, to Europe as a special envoy to work with Robert Livingston in negotiating the dispute with France. Jefferson proposes a "bargain" that will result in the acquisition of the Louisiana Territory. In a confidential message to Congress, Jefferson seeks $2,500 to send a small party of men to explore the Missouri River. Congress concurs, and Jefferson's secretary Meriwether Lewis will lead the expedition. Settling the boundaries with Native American lands is a major theme of the volume. In reality, "settling" results in major cessions of Indian lands to the American government. During the months of this volume Jefferson never leaves the capital, even for a brief sojourn at Monticello. He does, however, enjoy a visit of six weeks from his daughters and two of his grandchildren. They participate in Washington society, capture the affection of Margaret Bayard Smith, and brighten Jefferson's days.

Volume 38 opens on 1 July 1802, when Jefferson is in Washington, and closes on 12 November, when he is again there. For the last week of July and all of August and September, he resides at Monticello. Frequent correspondence with his heads of department and two visits with Secretary of State James Madison, however, keep the president abreast of matters of state. Upon learning in August of the declaration of war by Mawlay Sulayman, the sultan of Morocco, much of the president's and the cabinet's attention is focused on that issue, as they struggle to balance American diplomatic efforts with reliance on the country's naval power in the Mediterranean. Jefferson terms the sultan's actions "palpably against reason." In September, he addresses the concerns of the mayor of New York City and the governor of South Carolina that free blacks expelled from Guadeloupe by the French will be landed onto American shores. Although he believes the matter will be dealt with by the states, he also instructs Secretary of the Treasury Albert Gallatin to direct custom house officers to be watchful. In late August, Jefferson is alerted that he has been touched by the "breath of Slander," when James T. Callender's accusations appear in the Richmond Recorder and make public his relationship with Sally Hemings. The president offers no comment, and a month later returns to Washington, where he continues planning for an impending visit by his daughters. Some images inside the book are unavailable due to digital copyright restrictions.

A definitive scholarly edition of the correspondence and papers of Thomas Jefferson Congress adjourns early in March, and Jefferson goes home to Monticello for a month. After his return to Washington, he corresponds with territorial governors concerning appointments to legislative councils. He peruses information about Native American tribes, Spanish and French colonial settlements, and the geography of the Louisiana Territory. He seeks the consent of Spanish authorities to a U.S. exploration along the Red River while asserting privately that Spain “has met our advances with jealousy, secret malice, and ill faith.” A new law extends civil authority over foreign warships in U.S. harbors, and he considers using it also to constrain privateers. Federalist opponents bring up “antient slanders” to question his past private and official actions. His personal finances are increasingly reliant on bank loans. He starts a search for a new farm manager at Monticello. Meriwether Lewis and William Clark write from Fort Mandan in April before setting out up the Missouri River. Jefferson will not receive their reports until mid-July. In the Mediterranean, William Eaton coordinates the capture of the port of Derna and Tobias Lear negotiates terms of peace with Pasha Yusuf Qaramanli to end the conflict with Tripoli. News of those events will not reach the United States until September.

Confessing that he may be acting "with more boldness than wisdom," Jefferson in November 1803 drafts a bill to create Orleans Territory, which he entrusts to John Breckinridge for introduction in the Senate. The administration sends stock certificates to France in payment for Louisiana. Relieved that affairs in the Mediterranean have improved with the evaporation of a threat of war with Morocco, the president does not know yet that Tripoli has captured the frigate Philadelphia with its officers and crew. He deals with never-ending issues of appointment to office and quarreling in his own party, while hearing that some Federalists are "as Bitter as wormwood." He shares seeds of the Venus flytrap with Elizabeth Leathes Merry, the British minister's wife. She and her husband, however, create a diplomatic storm over seating arrangements at dinner parties. Having reached St. Louis, Meriwether Lewis reports on the progress of the western expedition. Congress passes the Twelfth Amendment, which will provide for the separate election of president and vice president. In detailed notes made after Aaron Burr calls on him in January, Jefferson records his long-standing distrust of the New Yorker. Less than a month later, a congressional caucus nominates Jefferson for a second term, with George Clinton to replace Burr as vice president. Jefferson makes his first trials of the "double penned writing box" called the polygraph.