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Burr conspiracy and trial

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.

The same year, Burr was soundly defeated in his bid to be elected New York governor. During the campaign, Alexander Hamilton publicly made callous remarks regarding Burr's moral character. Burr challenged Hamilton to a duel, mortally wounding him on July 11, 1804. 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. Both indictments quietly died and Burr was not prosecuted. Also during the election, certain New England separatists approached Burr, desiring a New England federation and intimating that he would be their leader. However, nothing came of the plot, since Burr had lost the election and his reputation was ruined after killing Hamilton. In August 1804, Burr contacted British Minister Anthony Merry offering to cede U.S. western territory in return for money and British ships.

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. Other plotters included Ohio Senator John Smith and Irishman Harman Blennerhassett. 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. 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. On February 13, 1807, Burr was captured in Louisiana and sent to Virginia to be tried for treason.

Burr's 1807 conspiracy trial became a national issue. 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 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. Instead, Jefferson provided relevant legal documents. After a three-month trial, the jury found Burr not guilty, while Jefferson denounced his acquittal. 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".