Washington ? Watching President Obama’s compelling speech on counterterrorism policy Thursday, you couldn’t help wondering what he might accomplish if he could apply the same intellectual focus and intensity to governing the nation that he has shown as covert commander in chief. 

By announcing new restraints on the use of armed drones for targeted killing and pushing again for the closure of the Guantanamo prison, Obama signaled more strongly than ever that he means to turn the page of American history that began on Sept. 11, 2001.

“This war, like all wars, must end,” he said in the signature line of the speech. He said he wants to amend or repeal the 2001 Authorization for Use of Military Force, the catch-all legal justification for the global war on terror. He wants to take America off its permanent war footing so that presidents have to justify future use of force prudently, on a case-by-case basis.

Stating this new reality required intellectual clarity, and it took guts, too. It’s a paradox that this president, with such limited management and political experience, has been so sure footed in the realm of secret warfare — knowing when to step it up, as he did with drone strikes and the May 2011 raid that killed Osama bin Laden, and knowing when to step it down, as he now proposes to do.

An unscripted Obama moment came when a heckler interrupted his review of the nation’s most sensitive intelligence problems, and the president didn’t lose a step — defending not just the heckler’s right to speak but much of her critique of how America’s policies are unintentionally damaging the country.

It bothers Obama that he inherited a red-hot rhetorical war on terror from George W. Bush, but one framed on loose rules and policy assumptions about a long (i.e., endless) war. He’s taken down the rhetoric and tightened the rules — wise on both fronts.

Some policies are still fuzzy. The president says he wants to move away from “signature” drone strikes and target only those who pose a “continuing and imminent threat” to Americans, but not yet and not everywhere. He knows that “imminent” doesn’t mean instantaneous, and to protect Americans, he may take out a bomber thousands of miles away, and months in advance. For that unflinching recognition, he has the country’s thanks.

Many details are still to come: In the Afghan theater (which includes the tribal areas of Pakistan), he plans to use drones aggressively until U.S. combat forces leave in 2014. What does Pakistan say about this? The president wants to move drones from the CIA’s deniable arsenal to the military’s more transparent framework, but he doesn’t explain how he’ll do that. He wants more oversight of targeted killings, but he has constitutional and practical objections to either a special court or an executive review panel. He wants to close the embarrassment of Guantanamo, but he can’t unless some members of Congress join him in showing some backbone.

Not a perfect plan for transition, but what the nation saw Thursday was a president who has taken to heart the warning he quoted from James Madison that “no nation could preserve its freedom in the midst of continual warfare.” That wariness of perpetual conflict doesn’t just apply to drones; Obama hasn’t yet seen a plan for U.S. military force in Syria that he thinks will work, so he’s refusing to sign off on one.

Obama understands the lonely predicament of leadership since 9/11: Nobody wants to challenge a presidential decision at the time it’s made, but everybody wants to second guess. He’s right that both sides of the equation must change.

In his wily role as covert commander in chief, Obama seems to have internalized the admonition of Bob Gates, his deeply cynical secretary of defense during the first term. Gates cautioned that “every day, someone, somewhere in the federal government, is screwing something up, and it could come back to bite the White House.” In running America’s secret wars, a Gatesian Obama tightened loose military and intelligence rules — but also decided to attack bin Laden knowing the 15 ways that disaster could strike.

The challenge for Obama, now that he has begun to “right-size” America’s counterterrorism policies to the actual threats, is to apply a similar rigor and toughness — combined with frank, public debate — to the larger problems of governing America. Watching Obama Thursday, you sensed that he still has the smarts and savvy to lead the country out of its dysfunctional mess, which is surely why the country re-elected him: So get on with it!