An impulsive adventurer, Aaron Burr, then fifty years old and living in Philadelphia, and still eager to acquire an empire, prepared a secret dispatch that was written in code and cipher and addressed to General James Wilkinson in July 1806. This was the famous letter that would lead President Thomas Jefferson to charge his former vice president and political enemy, Burr, with treason. On the basis of this dispatch, the cunning Wilkinson, who had become a secret, tenured, and well-paid informer ("Agent 13") of the Spanish government in the 1780s, warned Jefferson that a plot, led by Burr and described in the cipher letter, was under way to disrupt the United States and to take over Spain's colony, Mexico. Incidentally, Wilkinson's agent status, though long suspected, was finally documented by historians from records in the Spanish archives over a century later.

Wilkinson, with dreams of empire-building much like Burr, decided against a partnership in this enterprise, apparently designed by the two of them earlier. The troubled general betrayed his friend and collaborator likely in order to regain favor with Jefferson, who had just removed the unpopular Wilkinson from the governorship of the Louisiana Territory in May. Wilkinson's warning to Jefferson also served as evidence of his personal loyalty to the president and the United States, and indeed to Spain, whose North American empire was threatened.

Profound mystery surrounds the two copies of Burr's enciphered dispatch since Wilkinson admittedly falsified the original message, possibly changing passages that could be used as an indictment of Wilkinson. The general sent Jefferson his own plain text of Burr's letter, never producing the actual enciphered dispatch. The original dispatches in Burr's writing have never been discovered. Historians and biographers of Burr have given different decipherments of that enigmatic July 1806 letter: some of the sentences were based upon a book, possibly Entick's Pocket Dictionary, or Pron't [sic] English Dictionary, with page numbers and columns masked by unknown additives; moreover, the place and date of publication of the particular dictionary remain uncertain.

Like many of his political contemporaries such as Jefferson, Madison, and Monroe, and eager to hide his confidential letters from curious eyes, Burr occasionally turned to secret writing. In February 1801, he drafted a note in code to Congressman Edward Livingston and included a political code of 180 items, largely in numerical order, that provided Arabic numbers for the names of congressmen, states, cities, federal cabinet offices, and officers.^[118] In several instances, in an attempt to increase security, he assigned two different numbers for the same person: for example, Jefferson was "127" and "128" and Burr, "129" and "130."

On 22 July 1806, Burr had prepared two copies of his famous letter for General Wilkinson, a friend since their military days in the American Revolution. His lengthy relationship with the unscrupulous Wilkinson reflected his poor judgment of individuals. As Andrew Jackson remarked, "Burr is as far from a fool as I ever saw, and yet he is as easily fooled as any man I ever knew."^[119] One copy of Burr's letter was carried by a loyal supporter, Samuel Swartwout, who probably wrote the cipher in the original Burr letter, and a second copy was carried by another associate, Dr. Justus Erich Bollman. Each copy must have required three to five hours to encipher and encode exactly. Both copies reached Wilkinson, the former in October and the latter in November. The most recent biographer and defender of Burr argues that Wilkinson never received Burr's original letter: "The cipher letter as we know it today was not written by Aaron Burr. It was written by Jonathan Dayton."^[120] He contends that Dayton, a former senator from New Jersey, and collaborator with Burr, prepared two new letters and substituted them secretly for the ones carried by Swartwout and Bollman. No copy of the original letter in Burr's handwriting has been found, and Burr declared the dispatch provided to Jefferson by Wilkinson a forgery.

According to this fascinating account in the recent Burr biography by Milton Lomask, Dayton's copy included some of Burr's original sentences but included more flamboyant phrases about the exciting opportunities and strong auxiliary support for winning the new empire. Dayton hoped to increase Wilkinson's enthusiasm and backing for the expedition. Lomask conjectures that Dayton destroyed the authentic Burr letter.

Preparing the Burr original dispatch in code and cipher required the accuracy of a certified public accountant and the patience of a medieval monk. The secret system combined three complicated patterns of secret writing. One form, as noted above, was a book code, with a page number and word position in the column designated by two numbers, probably with the page number disguised by a specified additive and a line over the number referring to one of two columns on the page; the second number indicated the position of the word on the page. Secondly, Arabic numerals served as masks with "13," "14," "15," and "16" for Burr, and "45" for Wilkinson. Third, over sixty-six various symbols were used to represent letters of the alphabet and also various words. For example, a short horizontal line was a and a short vertical line, b; a square represented England, a square with a dot in the middle, France; a circle, President, and a circle with a dot in the middle, Vice President.^[121]

Briefly, the mysterious two-page Burr dispatch of July 1806, as deciphered by the editors of the Burr Papers, announced that funds for the expedition had been obtained and that six months provisions would be sent to locations named by Wilkinson. Further, groups would gather on the Ohio on 1 November and move to Natchez, meeting Wilkinson there in early December. "The people of the country to which we are go[ing] are prepared to receive us — their agents, now with me, say that if we will protect their religion and will not subject them to a foreign power, that in three weeks all will be settled. The god invite us to glory and fortune. It remains to be seen whether we deserve the boons."^[122]

Following Wilkinson's betrayal, Burr was tried in the spring and summer of 1807 in Virginia for a misdemeanor for organizing an expedition against a foreign colony, Mexico. Based on Wilkinson's accusations, the charge of treason was added by a grand jury, basing its decision upon a mistaken understanding of Chief Justice John Marshall's earlier obiter dicta in the trials of Burr's messengers, Swartwout and Bollman. A jury acquitted Burr of treason in September when it was shown that he had not actually participated in an overt act of levying war. The jury also ruled against the misdemeanor charge; however, Burr was to be sent back to the district court in Ohio. He never returned, and the government failed to press the law suit.

In July 1808, Burr sailed for England, and after several months visited Scotland before being expelled from Great Britain. Probably while in England, he prepared another code, this one for his correspondence with his only child, Theodosia. This curious mask would disguise the months and days and used almost fifty Arabic numbers, numerous pronouns, verbs, and amounts.^[123] A lengthy stay in Sweden and extended travel through Germany, France, Holland, and a return to England during the next three years, preceded his return to the United States a month before the War of 1812 with England broke out. Resuming the practice of law and his fascination with profitable business opportunities in the Latin American colonies and the later republics, Burr continued his energetic quest for adventure and economic power until his death on Staten Island in 1836.