In July of 1999, I met a young Army lawyer on a muddy farm field in southern Kosovo. His résumé (first in his class at West Point, Rhodes Scholar, Harvard Law) suggested that Major Mark Martins had his pick of private-sector jobs. But there was this tall and down-to-earth Ranger in a cramped tent, working late into the night. Days after NATO bombers forced Serbia out, Kosovo was scarred by civil war and ethnic strife. There was no government, no courts and effectively no laws. The military had to fill this gap and Maj. Martins was trying to sort out how. At the time, many thought troops were wasting time better spent on tank training in Germany. "We don't need to have the 82nd Airborne escorting kids to kindergarten," said Condoleezza Rice, then the foreign policy adviser to an ambitious Republican governor from Texas.

Fast forward a dozen years. Brig. Gen. Martins, 51, who deployed three times to Iraq, has just wound up a two-year tour in Afghanistan. Far from a distraction, Kosovo was a preview of things to come. The post-9/11 conflicts jolted the military out of the Cold War mindset for good and into the messy work of hunting terrorists, fighting insurgencies and, once again a dirty word in Republican presidential politics, nation-building in failed states.

Gen. Martins serves at the innovative wedges of this long war. He fashioned military-led efforts to provide Afghans and Iraqis with basic governance "in that difficult time that we call the meantime"—the months, usually years, from the collapse of the old regime to the rise of a functioning new state. In between, he helped "detoxify" (his words) American detention and interrogation policies in Afghanistan. He helped draft guidelines for U.S. military commissions adopted by Congress in 2009.

On Monday, a general whom Pentagon chief counsel Jeh Johnson calls a "superstar" begins as the chief prosecutor at the tribunals, which are gearing up to try Khalid Sheikh Mohammed and other terror suspects held at Guantanamo.

As the legal system struggled to adapt to the post-9/11 world, so did military doctrine. The army once favored "a hands-off approach" to civilian governance, says Gen. Martins. That was for the locals. But in the last decade, "important lightbulbs went off," he says. During the 2007 surge in Iraq, his commander and mentor, General David Petraeus, decided that to succeed, the military had to step in and help Iraqis deliver justice to their citizens. Gen. Martins set up "rule of law green zones" in seven Iraqi cities. U.S. forces secured courtrooms and protected judges and prosecutors. When Gen. Petraeus moved into Afghanistan last year to lead that surge, Gen. Martins got his own command, a Rule of Law Field Force, that built on the Iraq experiment. The U.S. had written new constitutions and set up legal systems in Japan and Germany after World War II. This was the first time that rule of law was at the heart of counterinsurgency.

The Afghan insurgency feeds off frustration with the ineptitude and rapaciousness of Kabul. "The Taliban is using the idiom of justice as its calling card and recruiting card," says Gen. Martins. "Afghanistan puts in very high relief the need for governance and dispute resolution—not the classic Western form of justice, but more resolution of disputes in a way that's seen as legitimate."

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