Secretary of State Thomas Jefferson was a supporter of the Jacobins, and really didn't believe the reports he received of the nightmarish violence in France. Jefferson, in a letter to James Madison, wrote that he would rather have "half the Earth desolated" than see the French Revolution fail. Even before 1793, Jefferson had linked the success of the French Revolution (what he thought was going on, anyway) with the success or failure of of his vision of America (Jefferson envisioned an Agrarian nation, with virtuous farmers as the backbone of America under a relatively weak central government).
While Jefferson and Madison were united w/ Washington and Hamilton concerning St. Domingue, they differed on France. Washington's decision to remain neutral in regards to the French Revolution signified to Jefferson that Hamilton had entered the sphere of foreign policy. In April 1793, Charles-Edmond Genet arrived in South Carolina; in quick order, this "Undiplomatic Diplomat" alienated and angered Jefferson, in that Genet proposed that U.S. ports be used for the needs of the French navy. Jefferson viewed Genet as all imagination with no judgment, as well as disrespectful (especially to Washington) and dictatorial.
One reason why Jefferson had reached his limit serving in Washington's Cabinet is that Alexander Hamilton meddled in the affairs of every department without apology. To Jefferson (and many others that worked with/around him), Hamilton was not a team player; in Hamilton's mind, he always knew best, and did what he wanted, most likely totally unaware of how his behavior was viewed by others.
According to Jefferson, Randolph didn't back him during his face-to-face tirade (a very rare display of temper) in a Cabinet meeting that was directed at Hamilton. To Jefferson, Randolph was a chameleon that changed his colors depending on the people who were around him. Actually, Jefferson was upset that Randolph didn't agree with him 100% of the time. This unrealistic expectation/perspective was mostly likely due to Jefferson's belief that Randolph was somehow interfering with his political war against Hamilton.
Added to Jefferson's travails was that Genet was still on the loose, doing everything he could to circumvent SecState Jefferson to pressure Washington to directly aid France. So dangerous did Genet become to Washington and his Cabinet that a memorandum was sent to Paris demanding that the government (what there was of it) recall Genet. When Robespierre came to power in France, Genet was recalled; Genet then asked Washington for asylum (Robespierre's directive was to send Genet back "in chains"). Washington graciously granted Genet's request, and Genet went to New York, married a member of the Clinton family (he was Governor), and lived the rest of his life in peaceful obscurity, never returning to France.
Approximately half of those that contracted Yellow Fever died, yet Secretary of State Thomas Jefferson refused to leave the city. Jefferson caught news that Hamilton had the fever, and he wrote Madison about what the SecTreas was going through with undisguised glee. In the same letter, Jefferson also speculated that Hamilton may be healthy, and using the epidemic as a ruse to build up sympathy and support for himself and his policies.
Hamilton, in fact, had contracted Yellow Fever, had barely survived, and was on the road to recovery when Jefferson had written his letter to Madison. Jefferson, after having "made his point" by being the only member of the Executive branch that chose to stay in Philadelphia and remained healthy during the scourge, left for Montpelier (Madison's home) in mid-September 1793. There, Jefferson, Madison, and James Monroe met to discuss their strategy in regards to Hamilton and the Federalists.
While not directed by Jefferson or Madison, the D-R Societies were all critical of Hamilton and his goals/policies (Also in 1793, New York became the most populous city with 33,000, surpassing Philadelphia).
Jefferson's & Madison's Republican Party and Hamilton's Federalist Party (they actually hadn't started to use that name for their party yet . . . anti-Republican was often used) both claimed legitimacy while labeling the other as a "Faction". The Federalists (and even Washington) went so far as to blame the D-R Societies for causing the Whiskey Rebellion of 1794 (pictured above). In the last quarter of 1793, Jefferson submitted his resignation as Secretary of State to President Washington, which would take effect on 31 December 1793; Washington reluctantly accepted Jefferson's resignation on 1 January 1794. Thomas Jefferson
retreated to Monticello, and waited for "The Call" from his party to return to the fray when the political landscape was more favorable.