Editing Thomas Jefferson (section)

==Presidency (1801–1809)==
{{Main|Presidency of Thomas Jefferson}}
[[File:Reproduction-of-the-1805-Rembrandt-Peale-painting-of-Thomas-Jefferson-New-York-Historical-Society 1.jpg|thumb|''Thomas Jefferson'', an 1805 portrait by [[Rembrandt Peale]]]]
Jefferson was [[First inauguration of Thomas Jefferson|sworn in as president]] by [[Chief Justice of the United States|Chief Justice]] [[John Marshall]] at the new [[United States Capitol|Capitol]] in Washington, D.C., on March 4, 1801. His inauguration was not attended by outgoing President Adams. In contrast to his two predecessors, Jefferson exhibited a dislike of formal etiquette. Plainly dressed, he chose to walk alongside friends to the Capitol from his nearby boardinghouse instead of arriving by carriage.<ref>[[#Peterson2002|Peterson (2002), p. 39]]</ref> His inaugural address struck a note of reconciliation and commitment to democratic ideology, declaring, "We have been called by different names brethren of the same principle. We are all Republicans, we are all Federalists."<ref>[[#Meacham|Meacham, 2012]], pp. 348–350.</ref><ref name=Peterson41/> Ideologically, he stressed "equal and exact justice to all men", minority rights, and freedom of speech, religion, and press.<ref name=Peterson_2002_p40>[[#Peterson2002|Peterson, 2002]], p. 40.</ref> He said that a free and republican government was "the strongest government on earth."<ref name=Peterson_2002_p40/> He nominated moderate Republicans to his cabinet: James Madison as secretary of state, [[Henry Dearborn]] as secretary of war, [[Levi Lincoln Sr.|Levi Lincoln]] as attorney general, and [[Robert Smith (Cabinet member)|Robert Smith]] as secretary of the navy.<ref name=Peterson41/>

Widowed since 1782, Jefferson first relied on his two daughters to serve as his official hostesses.{{sfn|Hendricks|2015|pp=21–22}} In late May 1801, he asked [[Dolley Madison]], wife of his long-time friend James Madison, to be the permanent White House hostess. She was also in charge of the completion of the White House mansion. Dolley served as White House hostess for the rest of Jefferson's two terms and then for another eight years as First Lady while her husband was president.{{sfn|Hendricks|2015|pp=21–22}}

===Financial affairs===
[[File:Albert Gallatin (by Gilbert Stuart).jpg|thumb|[[Albert Gallatin]], Jefferson's [[United States Secretary of the Treasury|Treasury Secretary]], depicted in a portrait by [[Gilbert Stuart]]]]

Jefferson's first challenge as president was shrinking the $83&nbsp;million national debt.<ref>[[#Meacham|Meacham, 2012]], pp. 352</ref> He began dismantling Hamilton's Federalist fiscal system with help from the secretary of the treasury, Albert Gallatin.<ref name=Peterson41>[[#Peterson2002|Peterson, 2002]], p. 41.</ref> Gallatin devised a plan to eliminate the national debt in sixteen years by extensive annual appropriations and reduction in taxes.<ref name="Peterson pp. 43-44">[[#Peterson2002|Peterson, 2002]], pp. 43–44.</ref> The administration eliminated the whiskey excise and other taxes after closing "unnecessary offices" and cutting "useless establishments and expenses".<ref name="Wood, 2010, p. 293">[[#Wood2010|Wood, 2010]], p. 293.</ref><ref>[[#Bailey2007|Bailey, 2007]], p. 216.</ref>

Jefferson believed that the [[First Bank of the United States]] represented a "most deadly hostility" to republican government.<ref name="Peterson pp. 43-44"/> He wanted to dismantle the bank before its charter expired in 1811, but was dissuaded by Gallatin.<ref>[[#Wills02|Wills, 2002]], pp. 50–51.</ref> Gallatin argued that the national bank was a useful financial institution and set out to expand its operations.<ref name="Peterson p. 44">[[#Peterson2002|Peterson, 2002]], p. 44.</ref> Jefferson looked to other corners to address the growing national debt.<ref name="Peterson p. 44"/> He shrank the Navy, for example, deeming it unnecessary in peacetime, and incorporated a fleet of inexpensive gunboats intended only for local defense to avoid provocation against foreign powers.<ref name="Wood, 2010, p. 293"/> After two terms, he had lowered the national debt from $83&nbsp;million to $57&nbsp;million.<ref name=Meacham387>[[#Meacham|Meacham, 2012]], p. 387.</ref>

===Domestic affairs===
Jefferson pardoned several of those imprisoned under the Alien and Sedition Acts.<ref>[[#Meacham|Meacham, 2012]], p. 357.</ref> Congressional Republicans repealed the [[Midnight Judges Act|Judiciary Act of 1801]], which removed nearly all of Adams's "midnight judges". A subsequent appointment battle led to the Supreme Court's landmark decision in ''[[Marbury v. Madison]]'', asserting judicial review over executive branch actions.<ref name="Meacham, 2012, p. 413">[[#Meacham|Meacham, 2012]], p. 375.</ref> Jefferson appointed three [[Associate Justice of the Supreme Court of the United States|Supreme Court justices]]: [[William Johnson (judge)|William Johnson]] (1804), [[Henry Brockholst Livingston]] (1807), and [[Thomas Todd]] (1807).<ref>[[#Urofsky|Urofsky, 2006]], p. viii.</ref>

Jefferson strongly felt the need for a national military university, producing an officer engineering corps for a national defense based on the advancement of the sciences, rather than having to rely on foreign sources.<ref>[[#Scythes1|Scythes, 2014]], pp. 693–694.</ref> He signed the [[Military Peace Establishment Act]] on March 16, 1802, founding the [[United States Military Academy]] at [[West Point, New York|West Point]]. The act documented a new set of laws and limits for the military. Jefferson was also hoping to bring reform to the Executive branch, replacing Federalists and active opponents throughout the officer corps to promote Republican values.<ref>[[#Scythes1|Scythes, 2014]], pp. 422–423.</ref>

Jefferson took great interest in the [[Library of Congress]], which had been established in 1800. He often recommended books to acquire. In 1802, Congress authorized Jefferson to name the first Librarian of Congress, and formed a committee to establish library regulations. Congress also granted both the president and vice president the right to use the library.<ref>{{Cite book|title=The Library: An Illustrated History|last=Murray|first=Stuart|publisher=Skyhorse Publishing|year=2009|isbn=978-0838909911|page=[https://archive.org/details/libraryillustrat0000murr/page/156 156]|url=https://archive.org/details/libraryillustrat0000murr/page/156}}</ref>

===Foreign affairs (1801–1805)===

====First Barbary War====
{{Main|First Barbary War}}
[[File:1800 map Afrique by Arrowsmith BPL 15210 detail2.jpg|thumb|alt=Map. Barbary Coast of North Africa 1806|The [[Barbary Coast]] of [[North Africa]] in 1806, including (left to right): [[Morocco]], [[Gibraltar]], [[Tunis]], and [[Tripoli, Libya|Tripoli]]]]

American merchant ships had been protected from [[Barbary Coast]] pirates by the [[Royal Navy]] when the states were British colonies.<ref>[[#Fremont-Barnes|Fremont-Barnes, 2006]], p. 32.</ref> After independence, however, pirates often captured U.S. merchant ships, pillaged cargoes, and enslaved or held crew members for ransom. Jefferson had opposed paying tribute to the Barbary States since 1785. In 1801, he authorized a U.S. Navy fleet under Commodore [[Richard Dale]] to make a show of force in the Mediterranean, the first American naval squadron to cross the Atlantic.<ref name="Meacham pp. 364">[[#Meacham|Meacham, 2012]], pp. 364–365.</ref> Following the fleet's first engagement, he successfully asked Congress for a declaration of war.<ref name="Meacham pp. 364"/> The "First Barbary War" was the first foreign war fought by the U.S.<ref>[[#CITEREFHerring2008|Herring, 2008]], p. 97.</ref>

[[Pasha]] of [[Tripoli, Libya|Tripoli]] [[Yusuf Karamanli]] captured the {{USS|Philadelphia|1799|6}}, so Jefferson authorized [[William Eaton (soldier)|William Eaton]], the U.S. Consul to [[Tunis]], to lead a force to restore the pasha's older brother to the throne.<ref>[[#Wood2010|Wood, 2010]], p. 638.</ref> The American navy forced Tunis and Algiers into breaking their alliance with Tripoli. Jefferson ordered five separate naval bombardments of Tripoli, leading the pasha to sign a treaty that restored peace in the Mediterranean.<ref>[[#Bernstein03|Bernstein, 2003]], p. 146.</ref> This victory proved only temporary, but according to Wood, "many Americans celebrated it as a vindication of their policy of spreading free trade around the world and as a great victory for liberty over tyranny."<ref>[[#Wood2010|Wood, 2010]], p. 639.</ref>

====Louisiana Purchase====
{{Main|Louisiana Purchase}}
[[File:Louisiana Purchase.png|thumb|The 1803 [[Louisiana Purchase]], completed during [[Presidency of Thomas Jefferson|Jefferson's presidency]], added {{convert|827987|lk=in|mi2|abbr=off}}, which doubled the geographic size of the United States.]]

Spain [[Third Treaty of San Ildefonso|ceded ownership]] of the Louisiana territory in 1800 to France. Jefferson was concerned that [[Napoleon]]'s interests in the vast territory would threaten the security of the continent and [[Mississippi River]] shipping. He wrote that the cession "works most sorely on the U.S. It completely reverses all the political relations of the U.S."<ref>[[#Meacham|Meacham, 2012]], pp. 383–384.</ref> In 1802, he instructed [[James Monroe]] and [[Robert R. Livingston (chancellor)|Robert R. Livingston]] to negotiate the purchase of [[New Orleans]] and adjacent coastal areas.<ref>[[#Wood2010|Wood, 2010]], p. 368.</ref> In early 1803, Jefferson offered Napoleon nearly $10&nbsp;million for {{convert|40000|mi2|abbr=off}} of tropical territory.<ref name=Freehling2005>[[#Freehling05|Freehling, 2005]], p. 69.</ref>

Napoleon realized that French military control was impractical over such a vast remote territory, and he was in dire need of funds for his [[The United Kingdom in the Napoleonic Wars|wars on the home front]]. In early April 1803, he unexpectedly made negotiators a counter-offer to sell {{convert|827987|mi2|abbr=off}} of French territory for $15&nbsp;million (~${{Format price|{{Inflation|index=US-GDP|value=15000000|start_year=1803}}}} in {{Inflation/year|US-GDP}}), doubling the size of the United States.<ref name=Freehling2005/> U.S. negotiators accepted the offer and signed the treaty on April 30, 1803.<ref name="Meacham387"/> Word of the unexpected purchase did not reach Jefferson until July 3, 1803.<ref name="Meacham387"/> He unknowingly acquired the most fertile tract of land of its size on Earth, making the new country self-sufficient in food and other resources. The sale also significantly curtailed European presence in North America, removing obstacles to U.S. [[Territorial evolution of the United States|westward expansion]].<ref name=Ellis208>[[#Ellis2008|Ellis, 2008]], pp. 207–208.</ref>

Most thought that this was an exceptional opportunity, despite Republican reservations about the Constitutional authority of the federal government to acquire land.<ref name="The Rise of American Democracy">[[#Wilentz|Wilentz, 2005]], p. 108.</ref> Jefferson initially thought that a Constitutional [[History of the United States Constitution#Senate changes|amendment]] was necessary to purchase and govern the new territory; but he later changed his mind, fearing that this would give cause to oppose the purchase, and urged a speedy debate and ratification.<ref>[[#Meacham|Meacham, 2012]], pp. 389–390.</ref> On October 20, 1803, the Senate ratified the purchase treaty by a vote of 24–7.<ref>[[#Tucker37|Tucker, 1837]], v. 2, pp. 152–154.</ref> Jefferson personally was humble about acquiring the Louisiana Territory, but he resented complainers who called the vast domain a "howling wilderness".<ref>[[#Peterson2002|Peterson (2002), p. 47]]</ref>

After the purchase, Jefferson preserved the region's Spanish legal code and instituted a gradual approach to integrating settlers into American democracy. He believed that a period of the federal rule would be necessary while Louisianans adjusted to their new nation.<ref>[[#Peterson70|Peterson, 1970]], p. 777; [[#Ellis2008|Ellis, 2008]], p. 230; [[#Wood2010|Wood, 2010]], p. 372.</ref>{{efn|Louisiana nevertheless gained statehood nine years later in 1812.<ref>[[#Wood2010|Wood, 2010]], p. 373.</ref>}} Historians have differed in their assessments regarding the constitutional implications of the sale,<ref>[[#Ellis2008|Ellis, 2008]], pp. 231–232.</ref> but they typically hail the Louisiana acquisition as a major accomplishment. [[Frederick Jackson Turner]] called the purchase the most formative event in American history.<ref name="Ellis208"/>

===Expeditions===
{{Main|Lewis and Clark Expedition|Dunbar and Hunter Expedition|Red River Expedition (1806)|Pike Expedition}}
[[File:Lewis and clark-expedition.jpg|thumb|alt=Corps of Discover on river boat October 1805|''Lewis and Clark on the Lower Columbia'', a 1905 portrait by [[Charles Marion Russell]] depicting [[Lewis and Clark Expedition|Lewis and Clark's expedition]] on the [[Columbia River]] during Jefferson's presidency]]

Jefferson anticipated further westward settlements due to the Louisiana Purchase and arranged for the exploration and mapping of the uncharted territory. He sought to establish a U.S. claim ahead of competing European interests and to find the rumored [[Northwest Passage]].<ref name="Ambrose76">[[#Ambrose|Ambrose, 1996]], pp. 76, 418.</ref> Jefferson and others were influenced by exploration accounts of [[Antoine-Simon Le Page du Pratz|Le Page du Pratz]] in Louisiana (1763) and [[James Cook]] in the Pacific (1784),<ref>[[#Ambrose|Ambrose, 1996]], p. 154.</ref> and they persuaded Congress in 1804 to fund an expedition to explore and [[:File:Lewis and Clark Expidition Map.jpg|map]] the newly acquired territory to the Pacific Ocean.<ref>[[#Rodriguez|Rodriguez, 2002]], pp. xxiv, 162, 185.</ref>

Jefferson appointed secretary [[Meriwether Lewis]] and acquaintance [[William Clark]] to lead the [[Corps of Discovery]] (1803–1806).<ref>[[#Rodriguez|Rodriguez, 2002]], pp. 112, 186.</ref> In the months leading up to the expedition, Jefferson tutored Lewis in the sciences of mapping, botany, natural history, mineralogy, and astronomy and navigation, giving him unlimited access to his library at Monticello, which included the largest collection of books in the world on the subject of the geography and natural history of the North American continent, along with an impressive collection of maps.<ref>[[#Ambrose|Ambrose, 1996]], pp. 54, 80.</ref> The expedition [[Timeline of the Lewis and Clark Expedition|lasted from May 1804 to September 1806]] and obtained a wealth of scientific and geographic knowledge, including knowledge of many Indian tribes.<ref>[[#Ambrose|Ambrose, 1996]], pp. 154, 409, 512.</ref>

Jefferson organized three other western expeditions: the [[Dunbar and Hunter Expedition|William Dunbar and George Hunter Expedition]] on the [[Ouachita River]] (1804–1805), the [[Red River Expedition (1806)|Thomas Freeman and Peter Custis Expedition]] (1806) on the [[Red River of the South|Red River]], and the [[Pike Expedition|Zebulon Pike Expedition]] (1806–1807) into the Rocky Mountains and the Southwest. All three produced valuable information about the American frontier.<ref>[[#Berry|Berry, 2006]], p. xi.</ref> This interest also motivated Jefferson to meet the Prussian explorer [[Alexander von Humboldt]] several times in June 1804, inquiring into Humboldt's knowledge of New Spain's natural resources, economic prospects, and demographic development.<ref>{{ cite book | last=Daum | first=Andreas W.|author-link=Andreas Daum | year=2024 | title=Alexander von Humboldt: A Concise Biography | location=Trans. Robert Savage. Princeton, N.J. | publisher=Princeton University Press |pages=80 | isbn=978-0-691-24736-6 }}</ref>

===Native American affairs===
{{Main|Thomas Jefferson and Native Americans}}
[[File:Black Hoof.jpg|thumb|left|[[Black Hoof]], leader of the [[Shawnee]], accepted Jefferson's Indian assimilation policies.]]

Jefferson refuted the contemporary notion that Indians were inferior and maintained that they were equal in body and mind to people of European descent,<ref>[[#TJF:Indians|TJF: American Indians]]</ref> although he believed them to be inferior in terms of culture and technology.<ref>{{cite web|url=https://www.monticello.org/site/jefferson/thomas-jeffersons-enlightenment-and-american-indians|title=Thomas Jefferson's Enlightenment and American Indians|publisher=Thomas Jefferson Foundation|access-date=July 10, 2024}}/</ref> As governor of Virginia during the Revolutionary War, Jefferson recommended moving the [[Cherokee]] and [[Shawnee]] tribes, who had allied with the British, to west of the Mississippi River. But when he took office as president, he quickly took measures to avert another major conflict, as American and Indian societies were in collision and the British were inciting Indian tribes from Canada.<ref name="Miller2008">[[#Miller08|Miller, 2008]], p. 90.</ref><ref name=Sheehan1974>[[#Sheehan74|Sheehan, 1974]], pp. 120–121.</ref> In Georgia, he stipulated that the state would release its legal claims for lands to its west in exchange for military support in expelling the Cherokee from Georgia. This facilitated his policy of western expansion, to "advance compactly as we multiply".<ref>[[#Peterson70|Peterson, 1970]], ch. 9.</ref>

In keeping with his [[Age of Enlightenment|Enlightenment]] thinking, President Jefferson adopted an assimilation policy toward American Indians known as his "civilization program" which included securing peaceful U.S.–Indian treaty alliances and encouraging agriculture. Jefferson advocated that Indian tribes should make federal purchases by credit holding their lands as collateral. Various tribes accepted Jefferson's policies, including the Shawnees led by [[Black Hoof]], the [[Muscogee]], and the Cherokee. However, some Shawnees, led by [[Tecumseh]], broke off from Black Hoof, and opposed Jefferson's assimilation policies.<ref>[[#TJFIndian Nations|TJF: President Jefferson and the Indian Nations]]</ref>

Historian Bernard Sheehan argues that Jefferson believed that assimilation was best for American Indians, and next-best was removal to the west; he felt that the worst outcome of the conflict would be their attacking the whites.<ref name=Sheehan1974/> Jefferson told [[United States Secretary of War|U.S. Secretary of War]] [[Henry Dearborn]], who then oversaw Indian affairs, "If we are constrained to lift the hatchet against any tribe, we will never lay it down until that tribe is exterminated or driven beyond the Mississippi."<ref>[[#morals|The Life and Writings of Thomas Jefferson]], pp. 265–266.</ref> Miller agrees that Jefferson believed that Indians should assimilate to American customs and agriculture. Historians such as [[Peter S. Onuf]] and Merrill D. Peterson argue that Jefferson's actual Indian policies did little to promote assimilation and were a pretext to seize lands.<ref>[[#Miller08|Miller, 2008]], p. 94.</ref>

===Re-election in 1804 and second term===
{{further|1804 United States presidential election}}
[[File:ElectoralCollege1804.svg|thumb|alt=Electoral College map|Results from the [[1804 United States presidential election|1804 U.S. presidential election]] in which Jefferson was reelected overwhelmingly to a second term as president]]

Jefferson was nominated for reelection by the Democratic-Republican Party, with [[George Clinton (vice president)|George Clinton]] replacing Burr as his running mate.<ref name=Meacham405>[[#Meacham|Meacham, 2012]], pp. 405–406.</ref> The Federalist Party ran [[Charles Cotesworth Pinckney]] of South Carolina, John Adams's vice presidential candidate in the 1800 election. The Jefferson-Clinton ticket won overwhelmingly in the electoral college vote, by 162 to 14, promoting their achievement of a strong economy, lower taxes, and the Louisiana Purchase.<ref name=Meacham405/>

In March 1806, a split developed in the Democratic-Republican Party, led by fellow Virginian and former Republican ally [[John Randolph of Roanoke|John Randolph]], who viciously accused President Jefferson on the floor of the House of moving too far in the Federalist direction, permanently setting Randolph apart [[Tertium quids|politically]] from Jefferson. Jefferson and Madison backed resolutions to limit or ban British imports in retaliation for British seizures of American shipping. Also, in 1808, Jefferson was the first president to propose a broad federal plan to build roads and canals across several states, asking for $20&nbsp;million, further alarming Randolph and believers of limited government.<ref>[[#Meacham|Meacham, 2012]], pp. 415–417.</ref>

Jefferson's popularity suffered further in his second term as a result of his response to wars in Europe. Relations with Britain deteriorated, due partly to the antipathy between Jefferson and British diplomat [[Anthony Merry]]. After [[Napoleon]]'s decisive victory at the [[Battle of Austerlitz]] in 1805, Napoleon became more aggressive in his negotiations with Jefferson and the U.S. over trading rights, which the U.S. proved unsuccessful in countering. Jefferson then led the enactment of the [[Embargo Act of 1807]], directed at both France and Britain, which triggered economic chaos in the U.S. and was strongly criticized, leading Jefferson to abandon the policy a year later.<ref>[[#Tucker37|Tucker, 1837]], v. 2, pp. 291–294.</ref>

During the American Revolution, colonial states abolished the international slave trade, but [[South Carolina]] reopened it. In his annual message of December 1806, Jefferson denounced the international slave trade as "violations of human rights" and called on the new Congress to immediately criminalize it. The following year, in 1807, Congress passed the [[Act Prohibiting Importation of Slaves]], which Jefferson signed.<ref>[[#Miller80|Miller, 1980]], pp. 145–146.</ref><ref name="Randal583">[[#Randall|Randall, 1994]], p. 583.</ref> The act established severe punishment against the international slave trade, although it did not address the issue domestically.<ref>[[#Kaplan|Kaplan, 1999]], p. 407.</ref>

In [[Haiti]], Jefferson's neutrality allowed arms to flow to the slave independence movement during the [[Haitian Revolution]], and Jefferson blocked attempts to assist Napoleon, who was defeated militarily in Haiti in 1803.<ref name=jstorhaiti>[[#JeffHaiti|Jefferson, Haiti ''The Journal of Southern History'' 61, no. 2 (May 1995)]], p. 221.</ref> But Jefferson's administration refused official recognition of Haiti during his second term, in deference to southern complaints about racial violence against slave holders. Recognition was not extended to Haiti until 1862.<ref>[[#Bernstein03|Bernstein, 2003]], pp. 146–147.</ref>

===Controversies===

====Burr conspiracy and trial====
{{Further|Burr–Hamilton duel|Burr conspiracy}}
[[File:Vanderlyn Burr.jpg|thumb|An 1802 portrait of [[Aaron Burr]] by [[John Vanderlyn]]]]
Following the 1801 electoral deadlock, Jefferson's relationship with his vice president, [[Aaron Burr]], rapidly eroded. Jefferson suspected Burr of seeking the presidency for himself, while Burr was angered by Jefferson's refusal to appoint some of his supporters to federal office. Burr was dropped from the Democratic-Republican ticket in 1804 in favor of charismatic [[George Clinton (vice president)|George Clinton]].

The same year, Burr was soundly defeated in his bid to be elected [[Governor of New York|New York governor]]. During the campaign, [[Alexander Hamilton]] made publicly callous remarks regarding Burr's moral character.<ref name=Chernow04_p714>[[#Chernow04|Chernow, 2004]], p. 714.</ref> [[Burr–Hamilton duel|Burr challenged Hamilton to a duel]], held on July 11, 1804. In the duel, Burr mortally wounded Hamilton, who died the following day. Burr was subsequently indicted for Hamilton's murder, causing him to flee to [[Georgia (U.S. state)|Georgia]], even though he remained president of the [[United States Senate|U.S. Senate]] during Supreme Court Justice [[Samuel Chase]]'s [[Impeachment of Samuel Chase|impeachment trial]].<ref>[[#Wood2010|Wood, 2010]], pp. 385–386.</ref> Both indictments quietly died and Burr was not prosecuted.{{sfn|Banner|1974|p=34}} 

In August 1804, Burr contacted British Minister [[Anthony Merry]] offering to cede U.S. western territory in return for money and British ships.<ref name="The Burr Conspiracy 2000">[[#TBC 2000|The Burr Conspiracy (2000)]]</ref> After leaving office in April 1805, Burr traveled west and conspired with Louisiana Territory governor [[James Wilkinson]], beginning a large-scale recruitment for a military expedition.<ref name=Peterson_2002_p50>[[#Peterson2002|Peterson, 2002]], p. 50.</ref> Burr discussed seizing control of Mexico or Spanish Florida, or forming a secessionist state in New Orleans or the Western U.S.; historians remain unclear as to his true goal.<ref>[[#Wood2010|Wood, 2010]], pp. 385–386; [[#Meacham|Meacham, 2012]], pp. 420, 422.</ref>{{efn|Further complicating matters, Wilkinson was posthumously revealed to have been in the simultaneous pay of the British, French, and Spanish.<ref>[[#Bernstein03|Bernstein, 2003]], pp. 161–162.</ref>}} In the fall of 1806, Burr launched a military flotilla carrying about 60 men down the [[Ohio River]]. Wilkinson renounced the plot and reported Burr's expedition to Jefferson, who ordered Burr's arrest.<ref name=Peterson_2002_p50/><ref>[[#Meacham|Meacham, 2012]], p. 420.</ref>{{sfn|Banner|1974|p=37}} On February 13, 1807, Burr was captured in Louisiana and sent to Virginia to be tried for treason.<ref name="The Burr Conspiracy 2000"/>
Burr's 1807 conspiracy trial became a national issue.<ref>[[#Appleby|Appleby, 2003]], p. 100; [[#Bernstein03|Bernstein, 2003]], p. 162.</ref> Jefferson attempted to preemptively influence the verdict by telling Congress that Burr's guilt was "beyond question", but the case came before his longtime political foe, and distant cousin, [[John Marshall]], who dismissed the treason charge. Burr's legal team subpoenaed Jefferson, but Jefferson refused to testify, making the first argument for [[executive privilege]].<ref>{{Cite web |title=John Marshall, the Great Chief Justice |url=https://law.wm.edu/about/ourhistory/John%20Marshall,%20the%20Great%20Chief%20Justice.php |access-date=April 9, 2025 |website=William & Mary Law School |language=en}}</ref> Instead, Jefferson provided relevant legal documents.<ref>[[#Bernstein03|Bernstein, 2003]], pp. 163–164; [[#Meacham|Meacham, 2012]], pp. 422–423.</ref> After a three-month trial, the jury found Burr not guilty, while Jefferson denounced his acquittal.{{sfn|Banner|1974|p=37}}<ref>[[#Bernstein03|Bernstein, 2003]], p. 165.</ref>{{efn|Burr then left for Europe and eventually returned to practicing law.}}<ref>[[#Appleby|Appleby, 2003]], p. 101.</ref> Jefferson subsequently removed Wilkinson as territorial governor but retained him in the U.S. military. Historian James N. Banner criticized Jefferson for continuing to trust Wilkinson, a "faithless plotter".{{sfn|Banner|1974|p=37}}

====Wilkinson's misconduct====
Commanding General [[James Wilkinson]] was a holdover of the Washington and Adams administrations. In 1804, Wilkinson received 12,000 pesos from the Spanish for information on American boundary plans.{{sfn|Banner|1974|p=35}} Wilkinson also received advances on his salary and payments on claims submitted to Secretary of War [[Henry Dearborn]]. This damaging information apparently was unknown to Jefferson. In 1805, Jefferson trusted Wilkinson and appointed him Louisiana Territory governor, admiring Wilkinson's work ethic.

In January 1806, Jefferson received information from Kentucky U.S. Attorney Joseph Davies that Wilkinson was on the Spanish payroll. Jefferson took no action against Wilkinson, since there was not then significant evidence against him.{{sfn|Banner|1974|pp=35–36}} An investigation by the [[United States House of Representatives|U.S. House of Representatives]] in December 1807 exonerated Wilkinson.{{sfn|Banner|1974|p=36}} In 1808, a military court looked into the allegations against Wilkinson but also found a lack of evidence. Jefferson retained Wilkinson in the [[United States Army|U.S. Army]].{{sfn|Banner|1974|pp=36–37}} Evidence found in Spanish archives in the 20th century proved Wilkinson was on the Spanish payroll.{{sfn|Banner|1974|p=35}}

===Foreign affairs (1805–1809)===

====Attempted annexation of Florida====
In the aftermath of the [[Louisiana Purchase]], Jefferson attempted to annex [[Spanish West Florida|West Florida]] from Spain. In his annual message to Congress, on December 3, 1805, Jefferson railed against Spain over Florida border depredations.{{sfn|Banner|1974|pp=37–38}}<ref name=Peterson2002p49>[[#Peterson2002|Peterson, 2002]], p. 49.</ref> A few days later Jefferson secretly requested a two-million-dollar expenditure to purchase Florida. Floor leader [[John Randolph of Roanoke|John Randolph]] opposed annexation, was upset over Jefferson's secrecy on the matter, and believed the money would end up going to Napoleon.<ref name=Peterson2002p49/>{{sfn|Banner|1974|p=38}} The Two Million Dollar bill passed only after Jefferson successfully maneuvered to replace Randolph with [[Barnabas Bidwell]] as floor leader.<ref name=Peterson2002p49/>{{sfn|Banner|1974|p=38}} This aroused suspicion of Jefferson and charges of undue executive influence over Congress. Jefferson signed the bill into law in February 1806. Six weeks later the law was made public. The two million dollars was to be given to France as payment, in turn, to put pressure on Spain to permit the annexation of Florida by the United States. France, however, refused the offer and Florida remained under Spanish control.{{sfn|Banner|1974|pp=38–39}}<ref name=Peterson2002p49/> The failed venture damaged Jefferson's reputation among his supporters.{{sfn|Banner|1974|p=39}}<ref name=Peterson2002p49/>

====''Chesapeake''–''Leopard'' affair====
{{Main|Chesapeake–Leopard affair}}
[[File:Leopardchesapeake.jpg|thumb|An illustration of [[HMS Leopard|HMS ''Leopard'']] (right) firing on the [[USS Chesapeake|USS ''Chesapeake'']] in June 1807]]

Starting in 1806, the Royal Navy began stopping American merchantmen to search for deserters from the British navy; approximately 6,000 sailors were impressed  into the Royal Navy this way, leading to deep anger and resentment among the U.S. public. In 1806, Jefferson issued a call for a boycott of British goods; on April 18, Congress passed the Non-Importation Acts, but they were never enforced. Later that year, Jefferson asked James Monroe and [[William Pinkney]] to negotiate an end to foreign interference with American merchant shipping, though relations with Britain showed no signs of improving. The [[Monroe–Pinkney Treaty]] was finalized but lacked any provisions regarding the issue of impressment, and Jefferson refused to submit it to the Senate for ratification.<ref name=Hayes505>[[#Hayes|Hayes, 2008]], pp. 504–505.</ref>

The British warship {{HMS|Leopard|1790|6}} [[Chesapeake–Leopard affair|encountered]] the {{USS|Chesapeake|1799|6}} off the Virginia coast in June 1807; ''Leopard'' fired at ''Chesapeake'' after the latter refused to allow for a search for deserters before removing four deserters from the ship.<ref name=embargo>[[#TJFEmbargo|TJF: Embargo of 1807]]</ref> Jefferson issued a proclamation banning British warships from U.S. waters. He presumed unilateral authority to call on the states to prepare 100,000 militia and ordered the purchase of arms, ammunition, and supplies, writing, "The laws of necessity, of self-preservation, of saving our country when in danger, are of higher obligation [than strict observance of written laws]". The {{USS|Revenge|1806|6}} was dispatched to demand an explanation from the [[Government of the United Kingdom|British government]], and Jefferson called for a special session of Congress in October to enact an embargo or alternatively to consider war.<ref>[[#Meacham|Meacham, 2012]], pp. 425–429.</ref>

====Embargo (1807–1809)====
{{further|Embargo Act of 1807}}
[[File:Ograbme.jpg|thumb|alt=A turtle biting a man carrying a barrel to a waiting ship|An 1807 political cartoon on the [[Embargo Act of 1807|Embargo Act]], depicting merchants dodging the "Ograbme", which is "Embargo" spelled backward]]

In December 1807, news arrived that Napoleon had extended the [[Berlin Decree]], globally banning British imports. The Royal Navy, meanwhile continued to impress sailors from American merchant ships. However, Congress had no appetite to prepare the U.S. for war; Jefferson asked for and received the Embargo Act, an alternative that allowed the U.S. more time to build up defensive works, militias, and naval forces. Meacham argued that the [[Embargo Act of 1807|Embargo Act]] was a projection of power that surpassed the Alien and Sedition Acts, and R. B. Bernstein said that Jefferson "was pursuing policies resembling those he had cited in 1776 as grounds for independence and revolution".<ref>[[#Bernstein03|Bernstein, 2003]], p. 168; [[#Meacham|Meacham, 2012]], p. 430.</ref>

In November 1807, Jefferson, for several days, met with his cabinet to discuss the deteriorating foreign situation.<ref>[[#Peterson2002|Peterson, 2002]], pp. 52–53</ref> Secretary of State James Madison supported the embargo,<ref>[[#Burstein10|Burstein, 2010]], pp. 497–498.</ref> while Treasury Secretary Gallatin opposed it, due to its indefinite time frame and the risk to the policy of American neutrality.<ref>[[#Meacham|Meacham, 2012]], p. 430.</ref> The U.S. economy suffered, criticism grew, and opponents began evading the embargo. Instead of retreating, Jefferson sent federal agents to secretly track down smugglers and violators.<ref>[[#Tucker90|Tucker, 1990]], v. 1, pp. 204–209, 232.</ref> Three acts were passed in Congress during 1807 and 1808, called the ''Supplementary'', the ''Additional'', and the ''Enforcement'' acts.<ref name=embargo/> The government could not prevent American vessels from trading with the European belligerents once they had left American ports, although the embargo triggered a devastating decline in exports.<ref name=embargo/>

In December 1807, Jefferson announced his intention not to seek a third term. He turned his attention increasingly to Monticello during the last year of his presidency, giving Madison and Gallatin almost total control of affairs.<ref>[[#Ellis96|Ellis, 1996]], p. 238; [[#Appleby|Appleby, 2003]], pp. 128–129.</ref> Shortly before leaving office in March 1809, Jefferson signed the repeal of the Embargo. In its place, the [[Non-Intercourse Act]] was passed, but it proved no more effective.<ref name=embargo/> The day before Madison was inaugurated as his successor, Jefferson said that he felt like "a prisoner, released from his chains".<ref>[[#Ellis96|Ellis, 1996]], p. 238.</ref>

===Cabinet===
{{Infobox U.S. Cabinet
|align=left
|Name=Jefferson
|President=Thomas Jefferson
|President start=1801
|President end=1809
|Vice President=[[Aaron Burr]]
|Vice President start=1801
|Vice President end=1805
|Vice President 2=[[George Clinton (vice president)|George Clinton]]
|Vice President start 2=1805
|Vice President end 2=1809
|State=[[James Madison]]
|State start=1801
|State end=1809
|Treasury=[[Samuel Dexter]]
|Treasury date=1801
|Treasury 2=[[Albert Gallatin]]
|Treasury start 2=1801
|Treasury end 2=1809
|War=[[Henry Dearborn]]
|War start=1801
|War end=1809
|Justice=[[Levi Lincoln Sr.]]
|Justice start=1801
|Justice end=1805
|Justice 2=[[John Breckinridge (U.S. Attorney General)|John Breckinridge]]
|Justice start 2=1805
|Justice end 2=1806
|Justice 3=[[Caesar Augustus Rodney]]
|Justice start 3=1807
|Justice end 3=1809
|Navy=[[Benjamin Stoddert]]
|Navy date=1801
|Navy 2=[[Robert Smith (Cabinet member)|Robert Smith]]
|Navy start 2=1801
|Navy end 2=1809
}}
{{clear}}