The presidential election of 1800 was one of the most dramatic political contests the United States has ever seen. James Madison's career was bound up in its outcome, although while the great controversy ensued, he awaited news updates at his home in Montpelier, suffering a bout of ill health. The main players in the contest–Thomas Jefferson, Aaron Burr, and Alexander Hamilton–were all men Madison knew personally and for whom he had strong feelings.

The presidential race began as a contest between the leader of the Federalists, President John Adams and the great representative of the Democratic-Republicans, Thomas Jefferson. Aaron Burr ran alongside Jefferson for the Vice Presidential spot. Jefferson won in the Electoral College seventy- three votes to Adams's 65. Since the College had not been designed with institutionalized political parties in mind, the government was thrown into confusion when Burr himself received seventy-three electoral votes. Following the Constitution, the election was sent to the House of Representatives, to see if Jefferson or Burr would become President. Federalists in the Congress supported Burr over Jefferson, seeing him as a less harmful Republican. For six days, neither candidate received majorities in the House.

The election was at a standstill until Alexander Hamilton came forward and, in a remarkable move considering his ideological opposition to Jefferson, supported the Virginian over his fellow New Yorker, condemning Burr as "deficient in honesty," and "the last man in the United States to be supported by the Federalists." Hamilton's influence and strong words tipped the scales in favor of Jefferson, who was finally elected on February seventeen, 1801, with Burr named as Vice President. When Jefferson finally took office on March 4, he named his old friend James Madison his Secretary of State.

The Madisons arrived in Washington on May 1, and lived in the White House until the fall, when they were given their own residence nearby. Madison's State Department consisted of ten men–the Secretary himself, his chief clerk, seven other clerks, and a messenger. Its chief preoccupation was foreign affairs, and Madison found his official business all-consuming. He worked very hard as Secretary of State, and also worked very closely with the President.

When Madison came into office, foreign affairs were relatively peaceful. Britain and France were headed toward agreement, with the Treaty of Amiens being negotiated. Problems arose, however, when Spain ceded back to Napoleon's France the vast stretch of land known as Louisiana, the middle portion of the area that is today the continental United States. This cession gave France control of much of the Mississippi River as well as the important trading port at the river's delta in the city of New Orleans. Jefferson and Madison both watched with apprehension, wondering whether Napoleon would send a fleet to the Mississippi to begin taking actual control of the territory. However, as war with Britain began to loom again for the French, no such action was taken.

Early in 1803, Jefferson sent James Monroe, a future president of the United States, to France to negotiate the Louisiana Purchase. Madison supervised the effort from the State Department, drafting the articles of the plan, and authorizing Monroe to offer a price starting from ten million dollars for the land. By mid-April, the French had agreed to the offer, and Monroe returned to America having been the agent for a virtual doubling in size of the territorial reaches of the United States of America. Madison was greatly satisfied by the outcome of the negotiations, as it gave his country total control of the Mississippi and strengthened America's power and independence from European influences.

While Madison was primarily occupied with foreign affairs during his years as Secretary of State, one major incident of internal import at this time involved him as a primary actor: the Marbury v. Madison decision of the Supreme Court, which set the precedent of judicial review of the other branches of the government. The State Department was, early in American history, in charge of delivering commissions to judges, and when Madison refused to deliver one to a certain William Marbury, Marbury sued the Secretary of State. The Supreme Court overruled Madison's decision, thus asserting a kind of judicial review over the executive branch of the government which would be a foundation for future decisions of a similar nature.

In President Jefferson's second term, foreign affairs became preoccupied with America's relations with Great Britain. In 1805, Europe was once again consumed by war, with Britain leading the fight against Napoleon's France. British ministers were angry that the United States refused to take sides in the conflict, and overlooked repeated acts of hostility by the British Royal Navy against American merchant ships. American seamen were taken captive and made to work on British ships, and American merchant ships were being plundered in American waters as well as on the high seas. Madison led a federal investigation of this problem, and by the end of 1807, he and President Jefferson had launched a policy of "commercial coercion," as Madison called it, whereby America refused to trade with Britain until they saw fit to curb acts of aggression against American merchant ships and sailors. On December twenty-two, the Embargo Act cut off American foreign commerce, and the Nonimportation Act against Britain kept away all British goods from American consumers.

A great deal of domestic opposition to the Embargo Act arose New England in 1808, and flavored the ideological battles of that year's presidential contest. Madison himself had emerged as the chief candidate for the Republicans, and he ran against the Federalist Charles Pickney and two other Republicans, George Clinton and James Monroe. Madison won the election by a wide majority, with Clinton becoming his Vice President.

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