AMERICAN HISTORY has no more paradoxical hero than Robert E. Lee. He led an armed rebellion against the authority of the United States yet emerged from the conflict the single figure admired and respected by both sides. He repeatedly mutilated the Army of Northern Virginia with his audacious penchant for attack, only discovering in the last year of the Civil War that his real gift was for defense, yet is widely if inaccurately regarded as one of the master tacticians of military history. He is worshiped as one of the great captains of the modern world, the peer of Caesar, Marlborough, Napoleon and Wellington, yet his greatest achievement was as an educator and a conciliator of venomously hostile factions.

That final aspect of his life is treated vividly and at length by Charles Bracelen Flood in his new biography. It is partial biography, however, confined to and tightly focused upon the five last years of Lee's life. Flood takes up the tale, in fact, the morning of Lee's surrender at Appomattox, a scene so familiar to most Americans it has become a kind of tableau vivant of the imagination; and as Lee leaves the famous sitting room of Wilbur McLean's house he rides off into a wholly new chapter of his life.

Yet matters began murkily and upon omens that would drive lesser men to despair. Lee's ride home to Richmond was across a moonscape of destruction and starvation. Richmond itself was a charred ruin. Lee, though almost universally revered, had little counsel to offer the hundreds who sought his help but to stop fighting, go home and try to resume a peaceable existence. He scarcely knew what he would do himself. He was almost penniless, the Federals had appropriated his wife's home, Arlington, and the single profession he knew--war--was now closed to him; and though he talked plaintively of establishing the family on a small subsistence farm he hadn't even the price of land. Nor was he willing to give his famous name to the commercial enterprises so eager to use it.

It was into this moral and practical vacuum, then, that the trustees of little Washington College in Lexington, Virginia, almost offhandedly dropped with their offer to Lee to assume the college presidency. After a few weeks of hesitation he accepted. The trustees, Flood makes clear, got a lot more than Lee's eminent reputation. He proved to be one of the great innovators of American education.

The college itself was in dreadful shape, damaged by Federal troops and reduced to a handful of students. Within a year Lee had turned it around, rebuilding its student body, repairing and adding to its plant, above all using his imagination to urge and support a variety of curricular reforms. Prior to his tenure, education at Washington College had been exclusively classical, in the fashion of the day. Lee asked for and got new programs in business, law, engineering and language, and the "press scholarships" he proposed proved to be the first systematic education in journalism anywhere.

Lee's vision was acute: a shattered South needed leaders of practical competence as well as chivalrous idealism (though Lee pushed idealism too), and the only sure way to get them was to see that education made them that way. It worked too: the college increasingly prospered under his sure hand (though it would languish again after his death), becoming eventually, as Washington & Lee University, one of the nation's preeminent private educational institutions.

The other part of the story is Lee's refusal to sulk over the South's defeat, or to encourage the rabid bitterness and revived sectionalism that followed Appomattox. His invariable advice to those who wanted, one way or another, to go on fighting was to accept defeat and make peace. Nor was this a merely negative quietism, for Lee's prestige was so high, throughout the country, that men more often than not did as he urged. It may be the central accomplishment of Flood's biography that he makes it clearer than in prior works how immensely influential Lee was between 1865 and 1870 in encouraging a spirit of national reconciliation.

He is less successful, in my view, in assessing Lee himself. The problem with all Lee biographies, as Thomas L. Connelly made evident in his 1977 study The Marble Man, is that a century of calculated hagiography has made Lee a figure of literally unbelievable perfection-- or as Douglas Southall Freeman put it, capping the sanctification, Lee "was one of the small company of great men in whom there is no inconsistency to be explained, no enigma to be solved."

We know better, and so must Flood. Evidence is abundant that Lee's marriage was unsuccessful. Perhaps because of his own father's ruin--"Light Horse Harry" Lee died a disgraced pauper--he was a severe and possessive father whose children displayed the wounds ever after. He had a violent temper, was famously stubborn (as Longstreet and Pickett learned to their sorrow) and despite his magnanimity could hold a grudge. He was an affectionate man too, however, and his intense crushes on beautiful women, as well as his infatuation with what nowadays we'd call ''nymphets," suggest a strongly sexed man who drastically repressed his emotions, perhaps to his medical disadvantage.

Flood acknowledges these things and never suppresses them, but more often than not he walks up to them only to turn away from their implications; and the end result is another biography more worshipful than penetrating. What made Lee tick? Washington, Jefferson, Lincoln and Franklin Roosevelt have undergone intense questioning from historians about their emotional complexities, and their stature survives. I believe Lee can survive too, as a great man but with warts, and that it's high time his biographers let him.y