Although Hamilton's life had been filled with extraordinary successes, the year 1797 marked a turning point in his life. From this point on until his death, Hamilton's life was plagued with scandal and political frustrations. His first pitfall struck in 1797, when James Monroe, who would later become president but was at this time a prominent Congressman from Virginia, denounced Hamilton as an adulterer. Monroe accused Hamilton of having an affair in 1791 and 1792 with Maria Reynolds while Hamilton's own wife was away in Philadelphia with their children, and of trying to bribe Reynolds's husband into keeping the affair quiet. Hamilton did, in fact, bribe James Reynolds, but he argued that the money he paid came out of his own pocket, and not out of the government's purse. Monroe had earlier pledged to keep quiet about the affair, but chose for unknown reasons to break his pledge in 1797. Hamilton wrote a public statement admitting his involvement in the extramarital affair, but continued to deny that he had used government funds to pay the bribe. Historians have since determined that James Reynolds had actually encouraged his wife to seduce Hamilton so that the family could make Hamilton purchase their silence.

Hamilton's public humiliation, however, did not hamper him from working. In the late 1790s, a conflict between France and the United States seemed inevitable. French naval ships had attacked hundreds of American merchant ships in the Caribbean Sea and Atlantic, and in 1798, President John Adams asked George Washington to resume his post as commander of the U.S. military. Washington consented, on the condition that Hamilton be named as his second-in-command. Adams agreed, and Hamilton eagerly accepted the assignment. He had been a lieutenant-colonel in the Continental Army but now served as a major-general.

Hamilton's primary duties as Washington's executive officer were to organize the troops and prepare for war with France. He made numerous recommendations to Congress on how best to improve the military. The thought of leading his country to war as a great military commander excited him greatly. He was sadly disappointed when, in early 1799, President Adams sent a peace delegation to France that ended the undeclared hostilities between the two countries.

In December of 1799, General Washington died. Hamilton had always admired Washington as a general, father figure, and friend, and the news of Washington's death stunned Hamilton. Without an enemy to fight or general to follow, Hamilton resigned his commission and returned to his law office in New York City.

As a lawyer, Hamilton focused his attention on his wealthier clients, mostly because he needed to pay for his new house in Manhattan. By this time, Hamilton had two daughters and five sons, but maintained an active public life as well. He founded a Federalist newspaper called the New York Evening Post, and later defended the editor of this paper in a libel suit that helped validate American's First Amendment, which grants freedom of speech.

Nor was Hamilton out of touch with the political scene, although his involvement in national and state politics worked to his disadvantage and disappointment. As the election of 1800 drew nearer, Hamilton found against all three of the presidential candidates. He disliked both Adams and Thomas Jefferson from his earlier political career, but he was especially opposed to Aaron Burr, a former lawyer from New York. Hamilton encouraged Federalists throughout the country to abandon their candidate, John Adams, and vote for Charles Pinckney, who had once served Washington. Hamilton's efforts against Adams worked the the advantage of the other two candidates, and both Adams and Pinckney were easily defeated, leaving Jefferson and Burr with an identical number of votes. Under the Constitution at this time, one of these remaining candidates was bound to become President and the other Vice President, while both candidates from Hamilton's own party were eliminated from holding either office.

Jefferson became the third president of the United States, and Hamilton's misfortune continued. In November of 1801, Hamilton's eldest son Philip was shot to death in a duel when he was only nineteen. Philip had agreed to the duel after arguing with a classmate at Columbia University about the virtues of his father versus those of Aaron Burr. Philip's death deeply shook his parents, and drove Hamilton's eldest daughter to insanity. When Mrs. Hamilton gave birth to another son, their sixth, they named him Philip.

In 1804, Vice President Aaron Burr turned to New York's upcoming gubernatorial election to make his next political mark. Under Jefferson, Burr had little actual power, and decided that his career would best be served by becoming Governor of New York. This appalled Hamilton, not only because of his personal opinions but also because he uncovered a plot by some Federalists in the northern states to use Burr as their candidate to help them secede from the Union. To ensure that Burr would not be elected, Hamilton published a series of essays denouncing Burr and the dissolution of the United States. These essays had little effect due to Hamilton's waning influence in the Federalist Party, but Burr was defeated a strong Republican campaign.

Burr's defeat could not be attributed to Hamilton, but Burr blamed him nonetheless, and challenged Hamilton to a duel. Hamilton accepted Burr's challenge, although he privately confessed that he did not intend to kill his rival. The two men and their seconds met in New Jersey at seven in the morning on July 11, 1804. Hamilton missed Burr, but Burr's bullet hit and fatally wounded Hamilton. Hamilton was brought back to New York, where he died the next day. He was only forty-seven years old.

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