John Jay arrived in Congress on December 5th, 1778. Silas Deane had been recalled from France for alleged corrupt dealings by Arthur Lee. In the summer of 1778, he attempted to clear himself but Congress sought to resolve the impasse not by calling back Arthur Lee to substantiate his claim but by tabling the matter. In his address, Deane indicted the conduct of his fellow commissioner Arthur Lee and obliquely challenged the authority of Congress. Samuel Adams, who had led the anti-French faction, with the help of President Henry Laurens, opposed Deane. Supporters of Benjamin Franklin, one of Deane's fellow foreign commissioners, came to his defense.
Jay stepped right in the middle of the controversy. He had been briefed by Gouverneur and Robert Morris that Deane, despite his exceptional contributions as a commissioner in France, was ill-treated by Congress. John Jay who was part of the “constructive party”, in fact, helped secure Deane's appointment. Delegate Jay regarded Deane as honest and patriotic and had little regard for the Lees due to a bitter dispute with Richard Henry Lee in the First Continental Congress. Jay also knew that the Lee-Adams Faction was responsible for General Schuyler's and Arthur St. Clair's loss of favor during the Campaign against Fort Ticonderoga and Saratoga. John Jay ardently supported Deane and therefore became a political opponent of then sitting President Henry Laurens.
President Henry Laurens was livid over Deane's public outcry and the President unsuccessfully attempted to have Congress censure Deane's publication. Laurens, for the third time, quit his office expecting Congress to reject his resignation. To Laurens surprise he was not asked to stay on as President by a majority vote of the delegates. Instead Congress called for a recess until the following day to vote for a new President.
The Continental Congress turned to Laurens adversary, John Jay only three days after taking his Delegate and elected him President of the Continental Congress on December 10, 1778. Eight states voting for Jay and four for Laurens.
