Jefferson told Madison that the battles seemed endless, and victories had been too elusive; in effect, TJ was making a political tactical retreat to Monticello. Jefferson may have been retreating to Virginia, but Democratic-Republican Societies were emerging and spreading in New England and New York in 1793.
These very aggressive pro-Jefferson / anti-Federalist groups were organized and led by working-class and middle-class citizens, and also featured a strong immigrant presence. These societies were viewed by Hamilton and President Washington as very dangerous groups that were a serious threat to the social order. By 31 December, 1793, the friction was too great for Jefferson, and he officially resigned as SecState to Washington; Washington officially accepted the resignation on 1 January, 1794.
Although Jefferson was happy at Monticello, he needed to be in the world of politics and consequence, which meant holding office, articulating beliefs, and championing Republicanism over Monarchy. In the Fall of 1795, the rising star of New York politics,
Aaron Burr (pictured), visited Jefferson at Monticello . . . in Burr, TJ had a potential rival to Hamilton in the state. When the Jay Treaty was ratified in 1795, Jefferson and his Republican Party had the issue they needed; it was a rallying point, leading to momentum and purpose. Jefferson felt he was close to being "summoned" in order to block the rise of Monarchy in America.
"Farewell Address" was published, and it opened the floodgates in terms of candidates pursuing the Presidency in the upcoming election. Jefferson wrote Madison that it might be best if he was elected Vice-President, given the current domestic and foreign policy issues.
Meanwhile, Hamilton hatched a strategy to try and keep BOTH John Adams and Thomas Jefferson from being elected (he thought Adams was too headstrong, and that Jefferson's vision of an Agrarian America was flat-out wrong). Hamilton urged key Federalist electors (with letter-after-letter) to vote for South Carolina's Thomas Pinckney (pictured). He hoped to deny Adams the Presidency by siphoning away several crucial electoral votes, while also costing Jefferson crucial Southern electors.
Jefferson knew that it would be a close call in 1796 between himself, Adams, and Pinckney; so much so that TJ asked Madison to be his advocate in case the election had to be decided in the House of Representatives. Madison, in at least one letter, told Jefferson that if he was elected Vice-President to accept it, arguing that "close proximity to the President critical."
Before the results were official, on 1 January, 1797, Jefferson sent Madison a draft letter addressed to Adams. It was very nice letter, pledging his support as Vice-President to President-Elect Adams. Madison sent a letter to Jefferson, basically scolding him as to the contents, and told him to NEVER send the letter, in that he believed that TJ needed to immediately set the tone of OPPOSITION! Later, as Washington exited the stage as President, Jefferson thought that GW was lucky to leave just before the bubble burst on the Federalists.
President Adams' Cabinet was a very mediocre group (with the exception of
John Marshall), which he inherited from Washington (GW wasn't very enamored with the group either). But that middling Cabinet gave their Adams a very hard time over making the offer to Madison via Jefferson; for the next four years, Adams never consulted TJ on a political question. Adams understood that he was being pressured to be a partisan President by powerful Federalists . . . and Jefferson came to understand that, even as VP, criticism was inevitable in politics.