After more than a month's deliberation in Congress, Jefferson had come to believe that "Congress had taken their ground firmly for continuing the embargo till June, and then war." Quite suddenly, however, the majority, frightened by threats of secession openly made by the New England members, and fearful of the famous Essex Junto, rallied to a compromise. Neither the people nor Congress were for war, and that fact had been clearly realized very early both by the French and the British ministers; at the same time it was felt that something must be done to relieve to some extent the financial distress of the Virginia planters and New England merchants. The result was that Congress decided to remove the embargo on March 4, "non intercourse with France and Great Britain, trade everywhere else, and continuing war preparations."[481]
On the first of March, three days before the inauguration of his successor, Jefferson signed the bill, but not without serious misgivings. The letters he wrote at that time contain even more convincing evidence that he did not expect the embargo to last much longer. To General Armstrong, the American representative in Paris, he declared on March 5 that "War must follow if the edicts are not repealed before the meeting of Congress in May." With Short, whom he had tried without success to have appointed Minister to Russia, he was more explicit if no less emphatic: "We have substituted for it (the embargo), a non-intercourse with France and England and their dependencies, and a trade to all other places. It is probable that the belligerents will take our vessels under their edicts, in which case we shall probably declare war against them."[482] Finally, to Madison himself, he wrote after reaching Monticello:
It is to be desired that war may be avoided, if circumstances will admit. Nor in the present maniac state of Europe, should I estimate the point of honor by the ordinary scale. I believe we shall, on the contrary, have credit with the world, for having made the avoidance of being engaged in the present unexampled war, our first object. War, however, may become a less losing business than unresisted depredation.[483]
Whatever may have been the opposition to the embargo and the opposition to Jefferson of disaffected Republicans, it is remarkable that he was able to keep his party in hand to the last minute and to choose his successor. Early at the beginning of his second term, he had expressed his irrevocable intention not to become a candidate for a third term. He was longing for his farm, his books, for the comforts of family life and he was not in the best of health.
Not only had he been troubled by rheumatism, but "periodical headaches" recurring at frequent intervals left him for days unable to write and hardly able "to compose his thoughts."
The Republicans had to make a choice between three possible candidates: George Clinton, Monroe, and Madison. The strongest argument that could be advanced in favor of the first was that, according to a precedent already apparently established, the Vice President was the logical successor, the "heir apparent", as Adams had termed it, to a retiring President. Moreover, Clinton could count on the support of the New York Republicans and had aroused no strong antagonism against himself. It soon became obvious, however, that the contest lay between the two Virginians and that the Virginia dynasty would not be broken as yet. Monroe was not without support in his native State and his candidacy had been upheld by a Republican caucus held by Randolph and his friends at Richmond; but another caucus of the Assembly had given a decisive majority to Madison. On January 23, 1808, a congressional caucus held in Washington pronounced decisively for Madison as President and George Clinton as Vice President. But Randolph held aloof and with his friends published a protest against the candidacy of Madison, who had "moderation when energy was needed", whose theories of government were tainted with federalism, "when the country was asking for consistency and loathing and abhorrence from any compromise." The danger of a split in the Republican Party was indeed serious, and while Jefferson reasserted his wish not to participate in any way in the campaign, he wrote to Monroe a long letter, deploring the situation and making an obvious appeal to his party loyalty. He warned him particularly against the passions that could not fail to be aroused in such a contest, and conjured him to keep clear "of the toils in which his friends would endeavor to interlace him."
That Monroe's amour-propre was deeply wounded appears in the letter he wrote in answer to his "chief." He complained lengthily and bitterly of having been handicapped by the sending of Pinkney and of the criticism to which he had been subjected on account of the treaty. Once again Jefferson had to soothe the discontent of his friend and "élève", which to a certain extent he succeeded in doing. It soon appeared, however, that the question would solve itself, that neither Monroe nor Clinton was strong enough to control the Republican majority. When the results came in, the Republicans had suffered the loss of all New England except Vermont, but Madison carried the election by one hundred and twenty-two votes, against forty-seven to C. C. Pinckney and six for Clinton. True enough, in several states the electors had been selected before the full pressure of the embargo was felt, but with such a substantial majority it is difficult to accept unreservedly Henry Adams' view that "no one could fail to see that if nine months of embargo had so shattered Jefferson's power, another such year would shake the Union itself."