Jefferson wasn't alone in his fight with Hamilton; his lifelong friend and political ally, James Madison, backed him all the way. If Jefferson was the leader of the opposition, which came to be known as "Democratic-Republican," Madison was his first lieutenant. (Federalists, Hamilton's allies, used to refer to Madison as the Republican General, and Jefferson as the Generalissimo.)
Madison understood what Jefferson was doing better than Jefferson himself did. Madison knew that Jefferson would return to politics: the stakes in the fight with Hamilton were just too high for Jefferson to remain on the sidelines forever. And it would take considerable effort to win that fight for good. In order to dismantle Hamilton's political program, it was going to take nothing less than a wholesale change in the government. If Hamilton couldn't be out-argued in president Washington's cabinet meetings, his program would have to be outvoted by the citizens. It was time for the Republicans to take over the government. And who better to head the take-over than the leader of the Democratic-Republican opposition? From the moment Jefferson left Washington's administration, Madison began to lay the groundwork for Jefferson's run for the presidency.
Presidential campaigns were very different then from the way they are now. For starters, no one could admit he wanted to be president. A gentleman wasn't allowed to ask someone for a vote; that was base. Others were supposed to spontaneously recognize his goodness, and chose to give him their vote. More importantly, most people didn't even get a vote. Presidential electors were chosen by state legislatures. The election cycle was therefore, long and uneven.
Winning required combining incredible political organization with the total denial of political aspiration. Luckily for Jefferson, in Madison he had the most able political organizer of the early American republic. As for the self-denial part, Jefferson had that down pat. He was at home in Monticello, rebuilding his manor house to better conform to his visions of Palladian architecture while sinking deeper into debt. He claimed to be wholly uninterested in politics, and completely engrossed in his farming. He would go on and on about his new plans for crop rotation to anyone willing to listen. But on some level, he must have known his performance was a sham. He prodded Madison to keep fighting Hamilton, and happened—ever so —conveniently—to meet often with the man who would become his running mate. Once the election cycle was clearly underway, he even predicted his own final vote total—quite a feat given the weirdness of the electoral system. Madison's expert organizing guided Jefferson to a second-place finish behind John Adams, a 3-vote loss, making him the country's next Vice President.
Jefferson had some qualms about reuniting with his longtime political partner. Jefferson and Adams had a long history. They had worked together on the committee charged with drafting the Declaration of Independence. They had been to Europe together to negotiate foreign treaties. They had served together in Washington's administration (Jefferson as secretary of state, Adams as Washington's VP). Even their families had become close; Abigail Adams, John's wife, was especially fond of Jefferson's daughters, and helped Jefferson care for them while he was in Europe. But the newly formed political parties had divided the two men. Adams, despite his own hatred of Hamilton, backed Washington's government, and had become one of the leaders of the Federalist Party, while Jefferson had become the leader of the opposition. Although Adams sought to pull Jefferson into his administration as a full partner, Jefferson, on Madison's advice, resisted. As Madison pointed out, it might be necessary for the Republicans to oppose Adams's plans, and that would be difficult to do if the Republican Party's leading figure seemed to share ownership of the administration's problems.
As a result, Jefferson played little or no role in John Adams's administration, even though, as vice-president, he was officially its second highest-ranking member. In fact, Jefferson's vice-presidency was among the most apparently apolitical periods in his life. He wrote a handbook of parliamentary procedure, and otherwise seemed dedicated to his studies. He had always been a bit of a naturalist; while in France, he had requested that two stuffed moose be sent to him in order to refute French claims that North American animals were weaker than their European counterparts. Now, as vice-president, he set himself about preparing a short paper on mammoth fossils to deliver to the American Philosophical Society. The Society's members even elected him their president. From the outside, Jefferson looked as disengaged a VP as Adams had been under Washington.
Behind the scenes, however, Jefferson was still vigorously engaged in the fight against the Federalists. He sponsored newspaper attacks on Federalist candidates. He encouraged congressional leaders to back Madison and opposed what he saw as the Federalists' anti-democratic tendencies. His clearest act of opposition was also his most secretive. By 1798, the increasingly violent wars in Europe were having a terrible effect on American shipping. Adams, spurred by the shameful treatment American diplomats received from France during the infamous XYZ affair, pushed the United States Navy to harass French vessels, leading the country into a "quasi-war" with France. When Republican newspapers, which had often been critical of Adams, turned up their venomous attacks, the Federalists passed the Alien and Sedition Acts, which severely restricted citizens' right to free speech and landed a number of Republican editors in jail. Jefferson, livid at what he saw as a gross abuse of federal power, joined with Madison to secretly author the Virginia and Kentucky Resolutions, which asserted a state's right to nullify federal laws it didn't agree with. Although the Resolutions did nothing to stop the implementation of the hated acts, they were to be important touchstones over the next eighty years in the ongoing debate over the relative importance of state and federal governments.
The failure of the Virginia and Kentucky Resolutions strengthened Jefferson's fighting spirit. The Federalists no longer needed to be opposed, he now felt; they needed to be destroyed—removed, root and branch, from the operation of the government. Jefferson entered the election campaign of 1800 ready for political war. The Federalists made his campaign easy. On 15 December 1799, George Washington, beloved leader of the Federalist Party, finally passed away. Without Washington to hold the party together, the two leading Federalist figures, Hamilton and Adams, launched vicious newspaper attacks against each other that damaged both their reputations. As the Federalist Party self-destructed, Jefferson and the Republicans won an easy, sweeping victory in the so-called "Revolution of 1800." Jefferson would finally have his chance to bring the Republic back to what he saw as the true "Spirit of 1776."