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The recent arrests of several top Taliban leaders in Pakistan is "detrimental to the strength and stability" of the insurgent movement in Afghanistan, but the war is still at a vulnerable stage, Gen. Stanley McChrystal said Friday.

As the largest U.S. offensive since the start of the war enters its fourth week in Helmand province, the first phase of routing insurgents from the major stronghold of Marjah is nearing its end.

But in a wide-ranging interview with Stars and Stripes, the top U.S. and NATO commander in Afghanistan stressed that the military success is just one in a series of steps, and said any hopes of stabilizing the country rest on cleaning up a corrupt government and convincing the Afghan people it provides a better future than the Taliban.

And the general pondered the recent crackdown on Taliban leaders in Pakistan after years of tacit acceptance.

In recent months, Pakistan’s intelligence service, or ISI, has worked with the CIA to arrest several key leaders of the Afghan Taliban in Pakistan, known as the Quetta Shura.

Among them was the group’s No. 2, Mullah Abdul Ghani Baradar, captured last month in Karachi. Former Taliban Finance Minister Agha Jan Mohtasim, considered a possible replacement for Baradar, was captured last week, The Associated Press and other news agencies reported.

"There have been a significant number of leaders arrested recently. And that is very detrimental to the strength and stability of the Taliban," McChrystal said. "If I was a young Taliban commander in Helmand right now under pressure, I would feel less confident if my senior leadership was being arrested right now at a high rate."

The general said he was still puzzling out why the ISI was suddenly cracking down.

"On face value, it’s absolutely a good thing, but I am still trying to gather information as to why it’s happened right now," McChrystal said.

The joint operations in Pakistan were outside the purview of McChrystal’s command over NATO forces. But as former commander of the Joint Special Operations Command, which oversees the military’s commando units, the general is well-versed in clandestine operations that often complement conventional forces.

And in a war focused on mentoring Afghan security forces and on trying to forge relations with a dubious Afghan population, there is a need for stealthy cross-border missions that target militant leaders.

"It’s a unity of purpose," McChrystal said.

But the big task of persuading a weary Afghan population in Marjah and elsewhere that the government is a viable alternative to the insurgency is just beginning.

"Everybody needs to sort of realize that phase of Taliban occupation is over," McChrystal said of Marjah. "Now they have got to be open to the government making its argument … that it can provide legitimate, adequate governance. And that will take time."

It’s a battle, he said, not just between armed forces, but between a potentially durable society with strong government and a coercive insurgency that feeds on frustration and the disaffected.

"There’s been enough pain in this country for 31 years, and enough problems with governance, enough problems with corruption, enough problems with warlords. So that is convincing people that enough substantive things have changed to warrant them to make a different judgment," he said.

"I think [the insurgents see] a more durable society that they are trying to undermine. But we are in a vulnerable period. It’s not yet durable there and it’s not durable in nearly enough places in Afghanistan."

The Marjah offensive is seen as the first big test of McChrystal’s counterinsurgency doctrine, stating forces need to hold and build an area after clearing it.

Marjah is the first of a number of "focus districts" identified by McChrystal’s command team as priority areas where establishing security is critical. McChrystal believes the 18-month surge in forces will help establish these secure areas.

But the general was quick to acknowledge that unless corruption is brought under control, the plan won’t work.

"This is not normal corruption," he said. "This is on a level that is deeply offensive to the Afghan people, particularly exercised by people in position of government or influence. There’s indignation on the part of the population against it."

McChrystal believes that although Afghanistan is 80 percent illiterate and most of the people are rural farmers living by tribal culture, Afghans have a natural tendency toward democracy.

"Afghanistan is an extraordinarily democratic society, although it doesn’t look and feel like it does in Massachusetts," he said. "What you have is Afghan leaders who absolutely consult the people through shuras (meetings) of local leaders. … So they do have the ability to have their voices heard, to demonstrate their frustrations."

Happy to answer questions about the war, McChrystal bristled at a question many soldiers have voiced: Why has he ordered the closing of Pizza Hut and Burger King franchises on the main bases?

The general said he believes the fast food joints were taking away from limited resources, including airfield usage, housing and electrical needs for the buildings and staff, and had other logistical concerns.

"I have a very difficult time losing priority of other key events, MRAP vehicles to keep people alive and things like that to bring in other things," McChrystal said. "Everything that Burger King takes competes with everything else on that post which we ration to everyone. So if you ask soldiers would you rather have Burger King or your mail, or would you rather have Burger King or enough ammunition, then it would be a more complete discussion."

Even soldiers not based near these facilities have voiced objection. It’s a slice of home, on the occasion when they do come back from the battlefield.

But McChrystal also said he thought it wasn’t fair that such luxuries were offered to troops at Bagram or Kandahar air fields, while those at outposts had to do without.

"We are still absolutely committed to things like Internet access, mail, gyms — all the things that are key for soldiers," he said. "But we have to draw priorities. And if I am the person that has to make the tough decisions, then I think that goes with the duty position that I’ve got."

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