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On a winter’s day nearly six years into America’s War for Independence, a messenger on horseback galloped toward Richmond carrying an urgent letter for Virginia’s governor. Ascending Shockoe Hill shortly after sunrise, the rider found Thomas Jefferson in the garden by his official residence, a modest townhouse.

The letter was alarming but cryptic. “A fleet of 27 sail” had been spotted entering the bay near Norfolk on December 30, 1780. Could they be invading British, headed for the James River and Richmond’s docks 100 miles upstream? Or were they the long hoped for French reinforcements? False alarms were frequent, and Jefferson was wary of agitating the state’s volunteer militia by calling them up unnecessarily. Just three months earlier, British ships had taken control of some Virginia coastal areas and seemed prepared to launch a full-scale attack. But the fleet turned its attention elsewhere, and many believed Virginia would be spared the large battles raging farther north and south.

So Jefferson stalled and on New Year’s Day sought more intelligence and consulted with legislators. Three days later, another messenger climbed Shockoe Hill and banged on Jefferson’s door at dawn. This time, there was no doubt. The British were coming—1,600 men led by the turncoat Benedict Arnold, a man Jefferson once admired. Arnold had already overtaken stunned, ill-equipped soldiers manning a half-built fort atop Hood’s Point, a strategic spot on the James River about 35 miles from Richmond.

Jefferson awakened his wife, Martha. They quickly packed their three young daughters off to Tuckahoe, a plantation 14 miles upriver where he had spent part of his childhood. Then, mounting his horse, he raced through Richmond to alert the militia.

For the next five months, as the British moved freely about Virginia, Jefferson spent much of his time staying one step ahead of the redcoats on his tail. And for the rest of his life, he spent much of his time defending his behavior during those five months. Critics denounced him as an incompetent military leader and a coward, wounding him so deeply that he once wrote he could only be salved by “the all-healing grave.”

After the nation, with much help from France, defeated the British at Yorktown, Jefferson remained so shaken by criticism of his leadership in those dark days that he renounced politics altogether and openly wrote that he would never seek office again. Yet 15 years later, he was back at it, as vice president and then president, and his lessons learned as a failed commander in Virginia were back too. For the eight years of his presidency, he fought to keep the United States out of wars looming on the horizon, writing, “I abhor war and view it as the greatest scourge of mankind.”

As the British fleet made its way from Hood’s Point to Richmond, Jefferson galloped six miles up the James River to Westham, the site of an arms factory. He had also ordered the transfer of important state papers there, but now feared that the town might come under attack. So he arranged to have seven wagonloads of arms and gunpowder moved across the river and buried. When he was satisfied that the arms and papers were secure, Jefferson mounted his horse again and rode another eight miles to Tuckahoe. He arrived at 1:00 a.m. and checked on Martha and their daughters—Patsy, 8, Maria, 2, and Lucy, a 5-week-old baby—before collapsing from exhaustion.

Meanwhile, perhaps 300 militiamen turned out in Richmond but had no chance of stopping a well-armed British force that was three times larger. For the rest of his life, Jefferson would be dogged by critics who accused him of dereliction of duty for failing to mount a defense of the city. “I was never off my horse but to take food or rest, and was everywhere my presence could be of any service,” Jefferson wrote later. “I may with confidence challenge any one to put his finger on the point of time when I was in a state of remissness from any duty of my station. But I was not with the army! true; for first, where was it? Second, I was engaged in the more important function of taking measures to collect an army; and, without military education myself, instead of jeopardizing the public safety by pretending to take its command, of which I knew nothing.”

Jefferson’s immediate concern was that the British would head to Tuckahoe as soon as they received intelligence on his whereabouts. So just after dawn he took his wife and daughters across the James and sent them eight miles further up, to a place called Fine Creek, where the Jefferson family owned property. Then he rode to Manchester, across the river from Richmond, where he took out his spyglass and watched the British swarm into the capital city. A long train of British and Hessian soldiers, horses, artillery and supplies emerged from a densely wooded road. After a brief fight with a small militia force, the British easily captured the capital. A British cannonball knocked off the top of a butcher’s house near the governor’s home, prompting the butcher’s wife and children to flee. British soldiers surrounded the townhouse, rounded up some slaves and tried to determine Jefferson’s location.

“Where is the governor?” a British officer—who may have been Benedict Arnold himself—demanded. The officer insisted he didn’t want to hurt Jefferson, but intended to take him as a prisoner, displaying a pair of silver-colored handcuffs he had brought for the occasion.

“He’s gone to the mountains,” responded one of Jefferson’s slaves.

“Where is the keys of the house?” the officer asked.

Mr. Jefferson left with them,” the slave replied.

“Where is the silver?”

“It was all sent up to the mountain,” the slave responded. In fact, he had hidden the silver throughout the house, including in the ticking of a bed and in the kitchen. Convinced that Jefferson had escaped, the soldiers began the business of plundering. They went into Jefferson’s cellar, broke off the necks from the bottles of the best wine and Antigua rum, and poured their contents into large barrels.

In the weeks that followed, as the British roamed throughout Virginia with little opposition, Jefferson increasingly came under attack even from some of his friends. John Page, who went to college with Jefferson and now was a militia colonel, was appalled at the state’s lack of readiness. “Arnold the traitor…has disgraced our country, my dear friend, so much that I am ashamed & ever shall be so to call myself a Virginian,” Page wrote to another militia leader. Edmund Pendleton, the former president of Virginia’s Committee of Safety, sent a scathing criticism of Jefferson’s action to George Washington, telling of “our disgrace in having Our Metropolis, at 100 miles distance from the Sea Coast, Surprized and taken without resistance by a handful of Banditti.” Pendleton wrote that Jefferson delayed calling out the militia until “it was too late” and had been “incredulous and not sufficiently attentive.” Pendleton told Washington that “it is only to you Sir, that I speak thus freely,” and urged that the general make “good use” of the information.

Jefferson’s most vocal critic was the Baron von Steuben, a fiery-tempered Prussian who served as a major general in the Continental Army and is credited with teaching patriot troops the essentials of military drill. Years later, a biographer described von Steuben as both “a systematic, circumstantial and deliberate liar” and the most influential officer during the Revolutionary War after Washington. He had arrived in Virginia just two months earlier to turn out Continental Army recruits and quickly concluded that the state was bereft of guns, clothing, supplies and qualified soldiers. One of his most urgent recommendations, which Jefferson supported, was to establish a major fort at Hood’s Point that could have been completed by a 40-man crew in less than a month. But construction was delayed by legislative bickering and Steuben was incredulous when Jefferson told him he did not have the authority to order militiamen or even slaves to do the work. Steuben angrily picked up his quill and wrote to Washington: “The Executive Power is so confined that the Governor has not in his power to procure me 40 Negros to work at Hood’s.” When Arnold arrived with his fleet the fort was a shell manned by perhaps 90 men.

Steuben had become Virginia’s military leader by default when the British invaded and soon would express his “disgust” with Jefferson’s inability to provide needed materiel or compel men into service after a general call for militia yielded only scattered groups of ill-equipped men. “If the powers of the State are inadequate to furnishing what is indispensably necessary, the Expedition must fail,” he wrote Jefferson. Time and again, Jefferson pleaded a lack of executive authority. Several years earlier, Jefferson had argued for a weak governorship out of fear that a strong executive might evolve into a tyrant. But he was also shackled by a recalcitrant legislature and a reluctant citizenry. He argued that he was balancing his limited powers as governor against the wishes of many Virginians who objected to impressment of property and enforcement of the draft and militia calls. “We can only be answerable for the orders we give and not for their execution,” Jefferson wrote. “If they are disobeyed from obstinacy of spirit or coercion in the laws, it is not our fault.”

After plundering Richmond and other nearby settlements, Arnold set about establishing a strategic British garrison at Portsmouth, near the mouth of the James River. With Arnold entrenched in Portsmouth, Jefferson called upon legislators to return to the partly destroyed capital city for an emergency session in which he hoped they would pass a measure compelling men to come out for militia duty to prevent “Invasions and Insurrections.” The proposal was defeated 32 to 17. Meanwhile the threat to Virginia continued to grow. A new British fleet commanded by General William Phelps and carrying 2,200 men suddenly appeared at the Capes of Virginia in March, and an army led by Lord Charles Cornwallis was on the move from South Carolina.

In the midst of the escalating crisis Jefferson’s baby daughter, Lucy, died just as an ice storm struck Richmond. He did not attend a meeting of the Governor’s Council, explaining that his wife was “in a situation in which I would not wish to leave her.” But he seemed to have experienced an epiphany about the need to assert his executive authority. Learning of mutineers in Hampshire County, Jefferson issued a chilling order: “Go and take them out of their Beds, singly and without Noise.” If they were not found the first time, Jefferson continued, “go again and again so that they may never be able to remain in quiet at home.”

The gathering of the British made it increasingly difficult to keep the government together.

Many legislators refused to come to Richmond, so the Assembly moved to Charlottesville, in the shadow of the Blue Ridge Mountains, which Jefferson long believed would be immune to attack. He had been even more certain that Monticello, his home on the outskirts of town, would be a safe haven.

Monticello was a crowded eight-room house in the midst of reconstruction when Jefferson and several senior legislators arrived in late May 1781. The governor and his family, along with servants and guests, crowded into rooms with unfinished, exposed brick walls and discussed the gloomy state of the Revolution. One delegate, John Breckenridge of Botetourt County, wrote to his mother, “We all fixed ourselves very comfortably, in full Assurance of being unmolested by the Enemy.”

In fact, the Green Dragoons under the much-feared British officer, Banastre Tarleton, were galloping towards Charlottesville and took control of the city just days after Jefferson informed the Assembly he no longer wanted to serve as governor after completing two one-year terms. Tarleton captured some legislators and dispatched an officer to see if Jefferson was still at Monticello.

By a stroke of great fortune, a friend of Jefferson happened to be at a tavern where British forces stopped on their way to Charlottesville. Jack Jouett, a 26-year-old militiaman who stood 6 feet 4 and weighed 220 pounds, wore a feathered hat and fancied himself one of the best riders of the Blue Ridge. Dashing along back roads, he arrived at Monticello and urged Jefferson to leave. Jefferson sent away his wife and children but tarried behind to collect state documents. “In preparing for flight,” Jefferson wrote, “I shoved in papers where I could.”

It was only after another Virginian warned Jefferson to leave that he finally fled. Minutes later, British forces arrived. They failed to find Jefferson, but they did discover some of his finest wine. Perhaps they raised a toast to King George III, since the raid on Monticello coincided with the monarch’s 43rd birthday.

Virginia was without leadership at its darkest hour. Jefferson not only was on the run, but his decision to vacate the governorship in the midst of a crisis outraged many Virginians. The legislature, which itself had fled over the Blue Ridge to Staunton, launched an investigation into Jefferson’s conduct, an extraordinary step believed to have originated with his Revolutionary colleague and predecessor as governor, Patrick Henry. Jefferson, who had retreated to a plantation he owned in southwest Virginia called Poplar Forest, promptly went to work on his defense and waited for the day that he would be allowed to explain his actions and restore his honor.

But on October 17, 1781, American forces, including members of Virginia’s much-criticized militia, defeated British forces at Yorktown, effectively ending the war in Virginia and laying the groundwork for the peace that would later be formalized. Jefferson demanded the right to answer his accusers in the legislature and, when no one stepped forward, he interrogated himself. Even though the Assembly issued a statement clearing him of blame and thanking him for his service, Jefferson was convinced that he would never again enter political life. He said he was “thoroughly cured of every principle of political ambition.” No “particle” of desire for political life remained. “Every fibre of that passion was thoroughly eradicated.”

Over time, the ambition resurfaced, as did his accusers.

When Washington declined to seek a third term as president in 1796, Jefferson let his name be put forward as a candidate. He had grown deeply disenchanted with efforts by Alexander Hamilton and other Federalists to build a strong central government and believed America was on a path to tyranny. For their part, Federalists sought to undermine his candidacy by reviving the controversy over his actions as wartime governor. One critic called Jefferson the “coward of Carter’s Mountain,” referring to the hill that he traversed while fleeing Monticello. Jefferson again felt compelled to defend himself, insisting that it would have been foolish to try to single-handedly take on a troop of British. He composed a chronology of the invasion, explaining that he vacated the governorship because he was “unprepared by his line of life and education for the command of armies” and believed that others were more qualified. But the attacks stung. John Adams, a Federalist, won the presidency and Jefferson became vice president, which afforded him little influence over policy.

After Adams built up the navy and army, Jefferson was concerned that the Federalists would goad the country into unnecessary battle and possibly destroy the young nation he had helped create. While he acknowledged his shortcomings as a military leader, he suggested that he had learned how to avoid a needless war and prevent the establishment of a “monarchical” government. So he ran for president again in 1800 and won, declaring he had ended the “reign of witches.” Jefferson considered his victory a second American Revolution.

During his two terms in office he withstood efforts by members of Congress to draw the United States into war against European powers, using declarations of neutrality, naval blockades and economic embargoes to avoid the call to arms. “I think one war enough for the life of one man,” he wrote. Nonetheless, he assured Americans during his presidency that should war be necessary, they would wage it “like men.” He authorized ships to attack the pirate fleet of the Barbary States, whose leaders had seized an American ship for a month and constantly demanded tribute from vessels for safe passage in the Mediterranean Sea. Jefferson emphasized the nation’s need for a strong system of defense, establishing a national military academy at West Point.

Still, critics continued to hound Jefferson about his actions as a wartime governor. The harshest accusations came from Henry “Light Horse Harry” Lee, the brilliant cavalry leader. Lee believed that Jefferson had put Virginia at risk by failing to call out the militia in a timely fashion. Had he been leading the forces in Virginia, Lee wrote in an autobiography published in 1809, he could have easily stopped Arnold. The state had more than enough militiamen “to have crushed any predatory adventure like that conducted by Arnold.” He mocked Jefferson for being driven out of Richmond, “forced to secure personal safety by flight.”

Jefferson called Lee’s charges a “tissue of errors” and was shocked that Lee’s book was considered by some a valid history of the war. Lee died in 1818 but Jefferson was still furious about the book in 1826 when Lee’s son, Henry Lee IV, contacted him about the possibility of a revised edition. Jefferson invited the younger Lee to Monticello, promising to provide documents that would exonerate him. When Lee arrived, he found Jefferson resting in bed. A clock, framed by two obelisks, hung from the wall at the foot of the bed. An Arabian sword also hung from one of the walls. Lee was shocked at Jefferson’s appearance. “There he was extended, feeble, prostrate,” Lee wrote. Jefferson expressed regret that Lee should find him “so helpless.” He alluded to his death “as a man would to the prospect of being caught in a shower, as an event not to be desired.”

Jefferson had spent hours in the previous months going over his records of the invasion, sorting the scraps of paper that he had taken with him as he fled on horseback from Arnold’s approach to Richmond. But Lee could not bring himself to conduct a tiring interview with an ill man and said he would return on another day. That day would never come. Lee was the last person outside Jefferson’s family circle to visit him at Monticello. He died less than a week later, on the Fourth of July, exactly a half century after the adoption of his Declaration of Independence. It had been an extraordinarily full life, helping to create a nation, establish principles of religious liberty, build a great university and serve two mostly peaceful terms as president. In the end, there were more than enough triumphs to overshadow the darkest period of his life, a time that haunted him, and shaped him, until the end.

Michael Kranish is the author of Flight From Monticello: Thomas Jefferson at War.

Originally published in the June 2010 issue of American History.