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Ultimately, Jefferson refused to run for a third term as President, and his chosen successor, James Madison, was elected President. Jefferson was happy to leave the presidency and never returned to Washington.
Unfortunately, the United States was soon drawn into another conflict with Britain by 1812. The same pressures that existed in 1807 were magnified in 1812. Republican Nationalist fervor pushed the country into war with Britain. The War of 1812 was ultimately a debacle for both the British in the United States. While Britain humiliated the US by occupying Washington DC and burning down a number of buildings that comprised the United States government, Britain's campaign in the United States was a mess. Britain was met with several military defeats and ended leaving the United States with its tail between its legs. The Treaty of Ghent provided an end to hostilities between the countries but neither side was happy.
The entire purpose of the Embargo was to demonstrate that there was potentially a new way to respond to aggressive warring European powers. That effort failed. Jefferson proved incapable of limiting smuggling by Americans that undermined his Embargo. Even though Southerners typically respected the Embargo, the failure to limit smuggling in the North hobbled the Embargo Act. Jefferson had essentially achieved all of the legislative goals he sought to accomplish during his Administration and the Embargo Act was one of his few clear failures.