You might think that so soon after the birth of the nation, things would be relatively peaceful, liberty would prevail and all would be well with the grand experiment. You would be wrong...
In 1796, when Washington was more than happy to leave the troubles of political dissent to someone else, the Federalists had become the target of significant public criticism from Jefferson and the Republicans. Events had helped to solidify party cooperation. Hamilton’s taxes, it should be remembered, were the result of a Federalist-supported treaty (negotiated by Federalist Chief Justice John Jay) approving the use of federal taxes to pay off British creditors from the war. The treaty infuriated supporters of local sovereignty and legislative primacy, including Jefferson. According to Beard, Hamilton was stoned in the streets while attempting to defend the treaty and "Jay was burned in effigy far and wide amid howls of derision from enraged Republicans." Americans had begun to experience the fruits of the new constitution. And many didn’t like what was happening.
Later, in an effort to destroy the Republican threat, Federalist newspapers, emboldened by the passage of the Alien and Sedition Acts, had begun to demand that "traitors must be silent," and the Federalist Gazette of the United States decreed that "He that is not for us is against us. It is patriotism to write in favor of government – it is sedition to write against it."
Jefferson, now regularly called a traitor by half the newspapers in the land, had had enough. Ferling recounts Jefferson’s impassioned plea against an unchecked federal government:
Jefferson took to his desk at Monticello…and wrote that the framers of the Constitutional Convention – delegates who represented twelve separate states, not the nation – had formed a "compact" to vest the national government with certain explicit powers but leave the "residuary mass" of the people’s "rights to their own self-government" within the states. Yet, Jefferson asked, who now was to determine if the national government had overstepped the bounds assigned to it in the Constitution? No "common judge" existed, and it would be ludicrous for federal authorities to be the "final judge of the extent of power delegated to itself." Each state would have to decide. Each state, he insisted, must have the authority to declare improper steps taken by the national government to be "void and of no force" within its jurisdiction. The vice president had drafted a doctrine of state nullification.
Knowing the rage these writings would produce in the minds of Federalists, Jefferson cloaked his personal support of these doctrines in secrecy. But, according to Ferling, Jefferson was confident that most Americans had never desired the kind of national government that the Federalists had been trying to impose on the public for a decade. He believed that time was running out for the Federalists.