During his second term, Jefferson's attention was focused on the trial of then former Vice President Aaron Burr for treason, which resulted in an acquittal, and on the issue of slavery, specifically the importation of slaves from abroad.

Despite the economic and political troubles caused by naval tensions with Britain, Jefferson was succeeded by his preferred successor in the form of James Madison.

[10] Before leaving office, the lame duck Adams, to the outrage of the Democratic-Republicans, at the last minute appointed many federal judges (mostly belonging to the Federalist Party) to fill positions created by the Judiciary Act of 1801.

Jefferson resisted the calls of his fellow Democratic-Republicans to remove all Federalists from their appointed positions, but he felt that it was his right to replace the top government officials, including the cabinet.

While serving on the Supreme Court, Chase had frequently expressed his skepticism of democracy, predicting that the nation would "sink into mobocracy," but he had not shown himself to be incompetent in the same way that Pickering had.

Determined to appoint a Democratic-Republican from a state unrepresented on the Court, Jefferson selected William Johnson, a young attorney who had previously served as an appellate judge in South Carolina.

Jefferson accepted visitors without regard to social status, discontinued the practice of delivering speeches to Congress in person, and enforced a less formal protocol at White House events.

[55] Two months after the expedition's end, Jefferson made his first public statement to Congress giving a one sentence summary about its success before asserting the justification for the expenses involved.

[67] For decades prior to Jefferson's accession to office, the Barbary Coast pirates of North Africa had been capturing American merchant ships, pillaging valuable cargoes and enslaving crew members, demanding huge ransoms for their release.

[70] Jefferson was reluctant to become involved in any kind of international conflict, but he believed that force would best deter the Barbary States from demanding further tribute.

[75] He initially planned to re-establish a French empire in the Americas centered around New Orleans and Saint-Domingue, a sugar-producing Caribbean island in the midst of a slave revolution.

[80] After Secretary of State James Madison gave his assurances that the purchase was well within even the strictest interpretation of the Constitution, the Senate quickly ratified the treaty, and the House immediately authorized funding.

[81] The purchase, concluded in December 1803, marked the end of French ambitions in North America and ensured American control of the Mississippi River.

[82] The Louisiana Purchase nearly doubled the size of the United States, and Treasury Secretary Gallatin was forced to borrow from foreign banks to finance the payment to France.

[85] Burr was indicted for Hamilton's murder in New York and New Jersey causing him to flee to Georgia, although he remained President of the Senate during Supreme Court Justice Samuel Chase's impeachment trial.

[85] After Aaron Burr was disgraced in the duel of 1804 and his own presidential ambitions were ended, he was reported by the British ambassador as wanting to "effect a separation of the western part of the United States [at the Appalachian Mountains]".

Jefferson believed that to be so by November 1806, because Burr had been rumored to be variously plotting with some western states to secede for an independent empire, or to raise a filibuster to conquer Mexico.

[89] After early 1802, when he learned that Napoleon intended to regain a foothold in Saint-Domingue and Louisiana, Jefferson proclaimed neutrality in relation to the Haitian Revolution.

The U.S. allowed war contraband to "continue to flow to the blacks through usual U.S. merchant channels and the administration would refuse all French requests for assistance, credits, or loans.

Historian Tim Matthewson notes that Jefferson "acquiesced in southern policy, the embargo of trade and nonrecognition, the defense of slavery internally and the denigration of Haiti abroad.

In 1806, he won congressional approval of a $2 million appropriation to obtain the Floridas; eager expansionists also contemplated authorizing the president to acquire Canada, by force if necessary.

[98] In keeping with his Enlightenment thinking, President Jefferson adopted an assimilation policy towards American Indians known as his "civilization program" which included securing peaceful U.S.–Indian treaty alliances and encouraging agriculture.

[99] When Jefferson assumed power, the Shawnee leader Tecumseh and his brother Tenskwatawa were leading raids against American settlements in the Ohio Valley, with munitions provided by British traders in Canada.

[107] American trade boomed after the outbreak of the French Revolutionary Wars in the early 1790s, in large part because U.S. shipping was allowed to act as neutral carriers with European powers.

[112] At the same time, the British gradually ended their policy of tolerance towards American shipping as the Royal Navy stepped up its blockade of hostile European ports.

Tensions with Britain heightened due to the Chesapeake–Leopard affair, in which HMS Leopard fired on USS Chesapeake in June 1807 after the latter refused a search for deserters from the Royal Navy.

With Burr having little chance at re-nomination, the party's congressional nominating caucus chose Governor George Clinton of New York as Jefferson's running mate.

[124] Randolph and other powerful Democratic-Republican leaders opposed to Madison, including Samuel Smith and William Duane, rallied around the potential candidacy of James Monroe.

[126] In the end, Madison headed off the intra-party challenges and defeated Federalist nominee Charles Cotesworth Pinckney, winning 122 of the 176 electoral votes in the 1808 election.

[129] In the 1930s, Jefferson was held in higher esteem; President Franklin D. Roosevelt and New Deal Democrats celebrated his struggles for "the common man" and reclaimed him as their party's founder.