By Michael Kranish

On July 4, 1776, Thomas Jefferson was writing at a table alongside other members of Congress in Philadelphia. This scene does not describe his work on the Declaration of Independence. Rather, he was taking notes on the nation's first congressional investigation - of American troops' disastrous campaign into Canada, in which Benedict Arnold played a leading role.

When the investigation was over a few weeks later, Jefferson remained one of Arnold's defenders, calling him a "fine sailor." Other revolutionary leaders were not so sure; one warned Jefferson that Arnold was "fiery, hot, and impetuous."

That turned out to be prescient. Less than five years later, the Revolution was on a razor's edge, and Arnold had turned traitor. In December 1780, he left British headquarters in New York with a fleet of 27 ships. His destination was Virginia, where an ill-prepared Jefferson was in his second one-year term as governor.

One of American history's most reviled men was on a mission against a state led by one of its most revered. The ensuing clash was one of the great yet strangely little-noted events of the Revolutionary War.

Arnold would gain the upper hand, repeatedly forcing Jefferson to flee the capital, Richmond. Other British forces later chased Jefferson all the way to Charlottesville. Eventually, he was forced to flee Monticello just minutes ahead of British soldiers, whose horses had galloped up his beloved mountain.

Jefferson refused a third term as governor, leaving the state leaderless at its darkest hour and causing even some of his friends to accuse him of cowardice.

It's worth remembering this extraordinary low point of Jefferson's life at a time when most people think of its high point - his authorship of the Declaration. Indeed, war continued for nearly seven years after the events of July 4, 1776. The uncertainty of the fight is vividly illustrated by the surprising scene of Jefferson himself hiding from the British on a plantation on the fifth anniversary of the Declaration.

In the seclusion of an overseer's cabin, Jefferson responded to accusations that he had left Virginia undefended. He acknowledged that he had no military training and was not the right man to lead Virginia in battle. But there was blame to go around; the militia was often reluctant to turn out, and the state's navy was nearly worthless, he wrote. He also noted, having learned that the legislature was preparing to investigate his conduct, that the wounds to his spirit would be cured only by the "all-healing grave."

Virginians were often unable to match British firepower in extended battlefield encounters, prompting the militia to retreat. At the same time, British forces divided to search the state for arms depots supplying forces in the Carolinas.

The British finally regrouped at a fateful place: Yorktown. Jefferson's successor as governor, Thomas Nelson, took to the battlefield and was reinforced by troops under George Washington and others.

The great American victory at Yorktown led Virginia's legislators to drop their inquiry into Jefferson's conduct. But Jefferson was adamant that he be allowed to defend his honor, and he addressed the assembly with a point-by-point rebuttal of the charges.

His honor restored, Jefferson said he did not have a "particle" of interest in reentering politics. Fortunately, this was a pledge he did not keep. The calamitous events of Jefferson's governorship haunted him for the rest of his life, but they also shaped the man who ultimately resumed public life with vigor and purpose.

Twenty years after Arnold's invasion, Jefferson sought the presidency, partly out of concern that the ruling Federalists were too eager to use the nation's Army against stronger European powers. Jefferson said he was ready to wage war if necessary - and he did use the Navy against pirates from Northern Africa - but he seemed intent on avoiding a broader conflict. He kept the country out of war with European powers during his two terms, even as he was harshly criticized for using embargoes and treaties to keep the peace.

Having helped begin the break from Britain, and having narrowly avoided capture by the British during his wartime governorship, Jefferson hoped the guns could be silenced. "We abhor the follies of war," Jefferson wrote a decade after the revolutionary conflict ended, "and are not untried in its distresses and calamities."

Michael Kranish is deputy chief of the Boston Globe's Washington bureau and the author of "Flight from Monticello: Thomas Jefferson at War" (Oxford, 2010). He can be reached via www.michaelkranish.com.