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.

V. 36. 1 December 1801 to 3 March 1802.

The Louisiana Purchase dominates the months covered in this volume. Jefferson departs for Monticello to enjoy a needed respite after the busy three and a half months he has just spent in the nation's capital. Shortly before leaving Washington, he has a last meeting with his cabinet, after which he issues a proclamation to reconvene Congress on 17 October, three weeks early. It is the "great and weighty" business of the French government’s stunning offer to transfer all of the Louisiana Territory to the United States that necessitates this important gathering. The event brings Jefferson enthusiastic congratulations from his friends and fellow Republicans. With Jefferson’s great success, however, comes the reality of getting the agreement with France approved and implemented. The boundaries of the territory ceded are not even clear. In private letters to his trusted advisers, Jefferson discusses the proper course of action. Should both houses of Congress be called to consider the French offer? Is it prudent to make the substance of a treaty public? And perhaps most vexing, does this executive action require an amendment to the Constitution? Some Federalists criticize the plan, but an expansion of the nation’s territory, proponents argue, will raise America’s stature in the eyes of the world. With the widening of the country’s borders, Jefferson’s project to send an exploratory party westward seems even timelier. William Clark accepts Meriwether Lewis’s invitation to join the expedition, and on the last day of August Lewis begins his journey down the Ohio River, the building of his boat finally complete.

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.

This volume opens on 4 March 1803, the first day of Jefferson's third year as president. Still shaken by the closing of the right of deposit at New Orleans, he confronts the potential political consequences of a cession of Louisiana to France that might result in a denial of American access to the Mississippi. But he resists pressures to seize New Orleans by force, urging patience instead. The cabinet determines in April that "all possible procrastinations" should be used in dealing with France, but that discussions with Great Britain move forward as well. In Paris, a treaty for the cession of the Louisiana Territory to the United States is signed, and in May the right of deposit is restored. On 3 July, word reaches Jefferson in Washington of the agreement that France has sold the entire Territory for $15 million. The glorious news, which may be the most momentous that Jefferson receives while president, appears in the National Intelligencer the following day. Having received congressional approval to send an expedition to locate a continental route to the Pacific, Jefferson drafts instructions and a cipher for Meriwether Lewis and arranges for the needed instruments. Following through on a promise to a friend to give his views of Christianity, Jefferson puts his religious creed on paper, a "Syllabus" of the morals of Jesus and the comparative merits of Christianity. He intends it only for a few trusted friends.

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.

After the congressional session ends, Jefferson leaves Washington and goes home to Monticello, where his ailing daughter Mary dies on 17 April. Among the letters of condolence he receives is one from Abigail Adams that initiates a brief resumption of their correspondence. While in Virginia, Jefferson immerses himself in litigations involving land. Back in the capital, he finds that he must reconcile differing opinions of James Madison and Albert Gallatin to settle a claim for diplomatic expenses. He corresponds with Charles Willson Peale about modifications to the polygraph writing machine. He prepares instructions for an expedition to explore the Arkansas and Red Rivers. William Clark and Meriwether Lewis send him maps and natural history specimens from St. Louis. Alexander von Humboldt visits Washington. News arrives that a daring raid led by Stephen Decatur Jr. has burned the frigate Philadelphia to deprive Tripoli of its use. Jefferson is concerned that mediation by Russia or France to obtain the release of the ship’s crew could make the United States appear weak. Commodore Samuel Barron sails with frigates to reinforce the squadron in the Mediterranean. Jefferson appoints John Armstrong to succeed Robert R. Livingston as minister to France and attempts to persuade Lafayette to move to Louisiana. In Paris, Napoleon is proclaimed Emperor of the French. Jefferson has “brought peace to our Country and comfort to our Souls,” John Tyler writes from Virginia.