Regional factionalism in the United States is nothing new: it reached its peak during the Civil War, and persists to this day in subtle economic and political manifestations (See the Civil War SparkNote). Jefferson's administrations were replete with factional intrigue and secessionist plots. And behind every scheme, or so it seemed, was Aaron Burr.
The first winds of secession were stirred by the Louisiana Purchase and its attendant increase in federal power. A group of New England Federalists aspired to bring New York down the road to eventual secession, and believed the support of Burr necessary to such an end. As sitting New York governor George Clinton had been named to replace Burr as Vice President on Jefferson's re-election ticket, a plan was concocted to elect Burr as governor of New York. From there, the secession could proceed as a bipartisan initiative.
It might have worked except for the fact that Alexander Hamilton, powerful as ever within the Federalist Party, blocked Burrs aspirations, not trusting his democratic tendencies. When one of Hamiltons letters impugning Burrs character was published, Burr challenged Hamilton to a duel, and Hamilton accepted. With this, on July 11, 1804, Burr shot Hamilton dead on an open plain at Weehawken, New Jersey, and immediately fled south to reassess his political future.
Meanwhile, Jefferson was suffering the abuse of another hostile election campaign. Heaps of abuse were piled upon him for his alleged affair with Sally Hemings and for his inconsistencies as a philosopher and a politician. Nevertheless, the vast majority of the public held the Louisiana Purchase in high esteem, choosing to value the acquisition of new lands as a more important factor than the corresponding defamation of the Constitution. In the national election, Jefferson won in a landslide, with 162 electoral votes to 14 for the Federalist candidate, Charles Pinckney. In a surprising turn of events, perhaps precipitated by the death of Hamilton, Jefferson carried every New England state except Connecticut, signaling the death knell of the Federalist Party and the near-total dominance of the Democratic-Republicans.
As leader of the unquestioned ruling party, Jefferson found himself with leeway to pursue his increasingly nationalistic agenda. In his Second Inaugural Address, Jefferson announced that the acquisition of new territory necessitated internal improvements and a stronger military force. Again, while these policies were in contradiction to his earlier stated views on states rights and limited federal authority, changing times called for changing measures. As Ralph Waldo Emerson later put it, consistency is the hobgoblin of little minds. By all measures, Jefferson's mind was anything but little.
During these middle years of his presidency, Jefferson spent a significant amount of time grieving for personal losses. First and foremost was the loss of his daughter Polly, who died from complications of childbirth at the age of twenty-four. More sinisterly, Jefferson lost his longtime friend and mentor George Wythe. Wythe, who had fathered a son by his slave mistress, was poisoned by a nephew who suspected that Wythe would favor the mulatto son in his will. Such an unusual turn of events must have weighed heavily upon Jefferson, who himself was entangled to various degrees with several mulatto slaves.