- "I hold it, that a little rebellion, now and then, is a good thing, and as necessary in the political world as storms in the physical."
- — Thomas Jefferson
Jefferson makes no appearance in Act One, as in this time frame he is in Paris, France.
Thomas Jefferson makes his first appearance in the beginning of Act Two. He returns home from Paris and is almost immediately confronted by a frustrated James Madison, who believes the financial plan proposed by Secretary Alexander Hamilton would only lead to complete government control ("What'd I Miss"). He then, along with Madison, debates with Hamilton and tries to convince the cabinet that the Hamilton financial plan was nothing less than empowering government control, leaving no say to the people. Washington eventually agrees and tells Hamilton that he needs votes before the plan would be put to action ("Cabinet Battle #1").
During the Compromise of 1790, Jefferson and Madison meet with Hamilton to discuss the plan and compromise; Jefferson would allow the plan if Hamilton voted for changing the nation's capital to a site closer to Jefferson's and Madison's homes ("The Room Where It Happens").
In a second cabinet meeting, Jefferson and Hamilton debate on whether the United States should assist the French in their revolution. Jefferson believed they should keep to their word as they promised in the Battle of Yorktown, however Hamilton thought they should go back on their oath and restrain from giving them military support; once again, Washington ultimately agrees with Hamilton ("Cabinet Battle #2"). This leads to Jefferson, along with Madison and Burr, to become indignant about the unwavering support Hamilton received from President George Washington and the three plotted to ruin Hamilton's political image ("Washington On Your Side").
The three men find the transactions between Hamilton and James Reynolds, and, not knowing Hamilton and been blackmailed by Reynolds and thinking Hamilton had stolen money from the government, Jefferson confronts Hamilton with the amounts. Hamilton reveals to them his affair that led to the blackmail and that it was his own money but did not believe Jefferson and the other men would keep it to themselves ("We Know"). However, Jefferson is taken aback as Hamilton goes further as to publish the affair in a public document to evade dishonor but destroy his private reputation in the process ("The Reynolds Pamphlet").
The year is 1800, and Adams drops out of the presidential election. The votes are narrowed onto Jefferson and Aaron Burr; Jefferson is surprised as Hamilton publicly promotes him and gives Jefferson his vote, though the two have never agreed, and effectively ruins Burr's change at the election in the process. Jefferson then wins the Election of 1800 ("The Election of 1800").
His last appearance is in Who Lives, Who Dies, Who Tells Your Story when he admits that "his financial system is a work of genius" after he has tried undoing it on several occasions.