The election of 1800, in which John Adams sought to be reelected, would prove to be a nasty fight. The New England Federalists again aligned themselves with Adams and Charles Pinckney of South Carolina, much to the anger of the Hamiltonian Federalists. The Republicans, now called the Democratic- Republicans, again nominated Thomas Jefferson and Aaron Burr. However, Alexander Hamilton campaigned for Pinckney for president and against Adams, drawing away much-needed support. In a decidedly ill-suited move, Hamilton published a pamphlet in the spring of 1800 attacking Adams' fitness to be president. The Federalist Party lay in tatters. In a quirk of the Electoral College, Jefferson and Burr mistakenly tied for the presidency–forcing the election into the House of Representatives, where Jefferson was chosen President.

Adams was crushed. Hamilton had blocked him at every turn, campaigned against him for two elections, and tried to steal Adams' Cabinet out from under him as Hamilton went about his warmongering. In short, every problem of Adams' administration could be traced directly to Hamilton, Adams felt. In all of his years of public service, the only man he could ever have been said to feel true hatred towards was Hamilton. Hamilton would be killed several years later during a duel with Aaron Burr.

In the closing months of John Adams' administration, he moved to the new capital, Washington, D.C., and into the presidential mansion, which would later be known as the White House. In the last moments of his administration, he appointed a cadre of Federalist judges to life-time spots in the judiciary–a move that became known as the "midnight judges." His judges included John Marshall, the future Supreme Court justice who would solidify the role of the powerful judiciary as only the best Federalists could have hoped. Embittered by his loss, Adams left office with a major breach of presidential etiquette: He left without attending Jefferson's inauguration and left behind only an abrupt note explaining a gift of "seven horses" to the President's House.

As Adams left office, he received word that his son, Charles, had died in New York City. The combination of his son's death and losing his much-loved place in public service crushed Adams. Despite feeling that his administration had accomplished "nothing," Adams had actually helped lay the groundwork for a powerful federal government, avoided a war with France, and expanded the military.

Adams returned to Braintree, where he expected to live out his final years in quiet solitude with his Abigail. He lived to be the oldest former president in history, almost ninety-one years old. From his family farm, he began an earnest letter-writing career, dispatching missives all over the country. Moreover, as time passed, his bitterness mellowed. Around 1812, Adams and Jefferson patched up their differences–by then they were among the last (and certainly the most famous) Founding Fathers–and began perhaps the greatest exchange of letters ever recorded in American History. Theologians, historians and philosophers alike treasure the Adams-Jefferson correspondence, carefully preserved by the two men. The two men grew quite close, discussing the course of the nation and their respective careers.

Adams only returned to the public sphere once, to assist at the Massachusetts Constitutional Convention in 1820. The Massachusetts constitution was a document that he had mostly written many decades before.

One of the proudest moments of the end of his life was living to see his son, John Quincy Adams, elected to the presidency in 1824–a move that Adams saw as a vindication of his own loss years before. He had by now buried four of six children and so took great pride in his son's achievements.

During the winter of 1826, Adams fell seriously ill, although he was able to keep writing to Jefferson until April. Both were invited to celebrate the Declaration of Independence's 50th birthday on July 4, 1826 in Washington, but Adams, almost ninety-one, and Jefferson, eighty-three, were too weak to attend. Ironically, both men died on July 4, fifty years after they so carefully crafted the document that gave birth to their United States. Adams' final words were, "Thomas Jefferson still lives!" But, sadly, Jefferson had died only hours earlier. America had lain to rest two of its greatest leaders and thinkers.