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Jones set off for St. Petersburg in May 1788, presented the Empress with a copy of the new U.S. Constitution, took command in the Black Sea and inflicted some hard blows on the Turkish fleet. He proposed going to the source by leading a Russian fleet into the Mediterranean, where it could interrupt Ottoman shipping between Constantinople and Egypt. For all this activity on the "infidel" side, Jones was rewarded by having a price put on his head by the ruler of Algiers. Meanwhile, however, he fell from favor at Empress Catherine's court and began to lose his health. Jefferson did not know this and had since become Secretary of State. In this capacity, he persuaded President George Washington to commission Jones to lead a delegation to Algiers, empowering him to give an ultimatum to the ruler. The package containing the commission and the instructions arrived in Paris only days after Jones had died there, in July 1792, from jaundice, nephritis and pneumonia. But Jefferson was still not discouraged.
The next year, 1793, saw Jefferson's retirement as Secretary of State and his withdrawal to Monticello. Like many of his temporary "resignations," this one was well timed. It meant that he did not have to express an opinion in the congressional debates on the military budget. Many of his Republican colleagues opposed the expense, as well as the principle, of having a permanent army and navy. The Federalist supporters of Adams, furthermore, desired a larger military budget in order to conduct hostilities against revolutionary France, a regime for which Jefferson felt sympathy. But by staying out of the political battle and biding his time, Jefferson ensured that when the hour struck for his own project, he could call on a fleet that Adams had built for him. In 1794, partly moved by the letters from American sailors held in Barbary dungeons and slave pens, Congress authorized the building of six frigates, three of which--the Constitution, the United States and the Constellation--were already completed. In July 1798 funds were approved for a Marine Corps as well.
Jefferson became President in early 1801, shortly after Yusuf Karamanli, the ruler of Tripoli, unwisely issued an ultimatum to the U.S.: If it did not pay him fresh tribute, he threatened, he would declare war on America. The new Commander in Chief coolly decided to let the ultimatum expire and take the declaration of war at face value. He summoned his new Cabinet, which approved the dispatch of a naval squadron and decided not to bother Congress--which was then in recess--with the information. He did not, in fact, tell the elected representatives of his plans until the fleet was on the high seas and too far away to be recalled.