Jefferson had not forgotten that twenty years before he had proposed that the seal of the United States should represent the Children of Israel led by a pillar of light. As much as the Puritans he was convinced that the American people was a chosen people, that they have been gifted with superior wisdom and strength, and this belief was just as much part of his creed of Americanism as it was the more openly expressed doctrine of more recent presidents of the United States.

With these brilliant and reassuring prospects before his eyes, Jefferson entered his second term. Little did he believe at that time that the four years before him were to be the most agitated and most distressing of his long career. The man whose fondest hope was to "secure peace, friendship and approbation of all nations" was to begin a series of police operations against the Barbary pirates of the Mediterranean and was confronted, at a time, with the possibility of a war with Spain, a war with England and a war with France. His philosophical toga was torn to shreds by the thorns strewn along the tortuous paths of international relations. At home he had to use all his ingenuity and resourcefulness to keep together disaffected elements in the Republican Party, to withstand the attacks launched in Congress by John Randolph of Roanoke, the impulsive, erratic and dangerous leader of the discontented Republicans. The man who had framed the Kentucky resolutions and had stood as the advocate of States rights was reproached with using his influence with Congress to pass the Embargo Act, "more arbitrary, more confiscatory" than any measure ever proposed by the Federalists. The man who had protested against the sedition bills had to repress the seditious attempts of the former Vice President of the United States. It seemed as if an evil genius had taken a malicious pleasure in making every effort to test the President in every possible way, and to confront him with the necessity of renouncing his most cherished principles. Jefferson did not come out of the ordeal without scars and deep wounds; but whatever may have been his deficiencies and his faults, whatever sins he may have committed, he kept his faith in the ultimate wisdom of public opinion and never tried to suppress by coercion the criticism to which he was subjected.

As a matter of fact, the roseate view of the situation presented by Jefferson in his second Inaugural Address was hardly warranted by facts. Even before the close of the first term, Randolph, who had been the standard bearer of the Republicans in the House, had shown signs of discontent. He had supported the "Remonstrance of the people of Louisiana", protesting that one of the essential provisions had been violated and that they should be admitted at once to "all the rights, advantages and immunities of citizens." On the other hand, Aaron Burr, even while remaining in office, had already paved the way for the dark and romantic machinations which were to culminate with his trial before Marshall at Richmond.

The story of Burr's conspiracy deserves a special place among American "causes célèbres." It has been told many times, and very vividly, but only the pen of Alexandre Dumas could do justice to it. Many efforts have been made to whitewash the memory of the chief conspirator, to throw most of the odium on Wilkinson and on Jefferson who, according to his enemies, would have gone out of his way to obtain the condemnation of a man who could not be proved guilty of any overt act, although there is no doubt that he had originated some of the most reprehensible schemes against the safety of his country. But Americans always had a foible for soldiers of fortune, for adventurers who dreamed of conquering new empires; for in them they see the magnification of the frontier spirit which for so long constituted one of the "pillars" of American civilization.

By an extraordinary trick of heredity, this adventurer, who should have been a Spanish conquistador, this arch plotter who had the insinuating ways of the Florentine, the tortuous and complicated mind so often considered as a privilege of the Europeans, was the great-grandson of Jonathan Edwards and of pure New England descent. He had fought bravely and enthusiastically in the Revolutionary War, he was a lawyer of no mean achievement; but his thirst for popularity, applause and success was beyond imagination, and this Machiavellic politician lacked in an extraordinary degree common sense and political vision. Had he withdrawn from the run for the presidency in time, had he gracefully accepted the second rank in December, 1800, he would have had a great political career before him. But to the last minute he refused to say the word that was expected from him; he accepted without protest the votes of the Federalists and was considered as a traitor to his party even before he took office. As early as January, 1804, he had gone to Jefferson and, after complaining that the President did not show him the same friendship as before, he had offered to resign at once if he were appointed to some foreign embassy. After Burr had left without obtaining any definite answer, Jefferson put down on paper a complete account of the conversation and dryly concluded:

I should here notice, that Colonel Burr must have thought that I could swallow strong things in my own favor, when he founded his acquiescence in the nomination as Vice-President, to his desire of promoting my honor, the being with me; whose company and conversation had always been fascinating with him etc.[452]

Disappointed in this respect, Aaron Burr turned his eyes towards New York, where he had worked so successfully during the preceding election. The post of governor happened to be vacant, and in February Burr was chosen by the discontented Republicans of the State to run for governor. It seems quite certain that, if he had been elected, the movement for secession already strong in New England would have received a new impetus and that a desperate effort would have been made to shake off "the rule of Virginia." When, after a savage campaign marked by invectives, brawls and riots, Burr was finally defeated, he could and did rightly attribute his failure to Hamilton who, from the very beginning, opposed his candidacy. A personal encounter was decided and the two adversaries met on the bank of the Hudson, pistol in hand, in a duel to the death. It has always been said that Hamilton did not take aim and fired first. Burr fired deliberately and Hamilton, fatally wounded, fell to the ground, to die the next day.

Found guilty of murder by a grand jury, and in fact already a fugitive from justice, Burr hid at first in Georgia and there concocted the most extraordinary plan to effect a separation of the western part of the United States with the help and financial assistance of England. Although evidence was not procurable at the time of his trial, there is no doubt that he thought the scheme feasible; that back in Washington, and when he was presiding over the impeachment proceedings of Judge Chase, the Vice President of the United States was prudently sounding the delegates of the western States, ingratiating himself to them and that the wildest dreams of empire were haunting his feverish imagination.

As soon as the session was over, Colonel Burr started out for a tour of the western States and, on an island of the Ohio, met by chance the philosopher-planter Blennerhasset, the innocent victim of his plots. Leaving Blennerhasset, Burr went to Cincinnati, Frankfort, Nashville. He met Andrew Jackson, the uncouth son of the frontier, and Wilkinson, the general in charge of the western territory. After a visit to New Orleans, where he was greatly elated by the discontent of the population, he went back to Saint Louis to discuss the situation with Wilkinson. Whether he still adhered to the original plan of separating the western from the eastern States is to a considerable degree doubtful. His immediate object seems rather to have been to lead an expedition of adventurers against Mexico, in case the war that was threatening between the United States and Spain should break out. It must be admitted that the plan in itself was not particularly objectionable to the Government, but it soon appeared that this scheme too had to be given up. After vainly attempting to secure assistance from the British Government, Burr, changing from conqueror to farmer, undertook to buy, with Blennerhasset, a grant of several hundred thousand acres on the Washita River, in Northern Louisiana, in order to establish there a model colony.

The rest of the story is well known. Rumors of a conspiracy grew in the West without disturbing at first the security of the Federal Government. Burr, summoned to appear before the district attorney of Frankfort, surrendered himself, but was twice discharged and continued his preparations for the settlement of Washita. Jefferson did not move until he received from Wilkinson a confidential message purporting to be the transcription of a ciphered letter sent by Burr. The President was so alarmed that he issued at once a proclamation, warning the people that a conspiracy had been discovered and directing the arrests of the conspirators and the seizure of "all vessels, arms and military stores." Wilkinson, eager to show his loyalty to the Government, arrested "without warrant" several emissaries of Burr. One of them was released, but two, Bollman and Swartwout, were sent out by sea to Baltimore and thence to Washington, where they were kept in the military barracks. In a special message to Congress, Jefferson apprised the Senate and the House of the facts "touching an illegal combination of private individuals against the peace and safety of the Union, and a military expedition planned by them against the territories of a power in amity with the United States, with the measures pursued for suppressing the same." (January 22, 1807)