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MARGARET WARNER: And for a closer look at the tensions in this crucial alliance, we’re joined by Shuja Nawaz, director of the South Asia Center at the Atlantic Council and author of its recent report, "Pakistan in the Danger Zone: A Tenuous U.S./Pakistan Relationship," and David Ignatius, a columnist for The Washington Post. He recently returned from a reporting trip to Pakistan.

And welcome back to you both. Shuja Nawaz, beginning with you, how serious is this rift over the helicopter raids and the blocked border crossing?

SHUJA NAWAZ, director of South Asia Center, The Atlantic Council: I think it reflects the general mistrust, which is pretty deep.

And it was extremely badly handled, I believe, by NATO and by the coalition. The apology that was tendered today could have easily been done at the very outset, which would have stopped the — the Pakistanis using the — the blockage of the convoys in Torkham. And it would have been resolved quite directly and immediately.

They missed an opportunity. They got caught in legalese. I believe, based on one report that I have received, that helicopters were actually returning back towards Afghanistan when they came upon this post on which they fired. If that is correct, then NATO should have been aware of that.

MARGARET WARNER: How do you read this David?

DAVID IGNATIUS, columnist, The Washington Post: Well, as your report showed, this is a week in which all the tensions that are in this relationship were evident.

Whenever I — I look at Pakistan and at the relationship, I — I try to caution myself that public pronouncements, public anger doesn’t tell you the whole story. The reality right now is that these are two countries that need each other badly, and they have a history of patching things together and muddling through.

And you would have to guess that, in this case, that will happen again. But I last week was in Pakistan. I had the experience two days before this helicopter attack in which members of the Pakistani Frontier Corps were killed by American fire visiting a training camp northwest of Peshawar in which U.S. special forces, sort of in secret, are training members of that same Frontier Corps to go out and fight in the tribal areas. So that shows the degree of complexity in this relationship.

MARGARET WARNER: Yes. Pakistan and the U.S. really are engaged in a covert war inside Pakistan, much more than either side acknowledges, right?

SHUJA NAWAZ: Yes. And, for quite a long time, the civilian government has been speaking out of both sides of its mouth, and it has actually inflamed public opinion, particularly regarding the drones. The — in September, we have had…

MARGARET WARNER: Which are the drone attacks, unmanned Predator drone attacks that have seen a huge increase in September.

SHUJA NAWAZ: Yes. In September, it was the largest ever number of attacks in any one month since the drone attacks began in the region.

But now, in recent months, the government had stopped using this as a stick to beat the U.S. with. And public opinion was gradually accepting them. But, clearly, now, with the timetable looming, the U.S. and the coalition is going to be forced into all these measures to regain momentum.

MARGARET WARNER: You’re talking about the timetable that President Obama has set to begin to dial back in Afghanistan, which is middle of next year.

SHUJA NAWAZ: Yes. Yes. And that’s going to create tensions within Pakistan, and particularly, as you reported, in North Waziristan, where they have a huge force presence, something like 35,000 men. But they haven’t moved against Haqqani.

MARGARET WARNER: The Haqqani Network, the al-Qaida-allied network.

So, David, is there essentially a fundamental difference between Pakistan and the U.S. over how to fight or to what degree to fight al-Qaida and its affiliates, or is it because the Pakistani military is stretched too thin?

DAVID IGNATIUS: Well, the Pakistani military says that’s why it can’t conduct the offensive in North Waziristan that the U.S. would like. And I think most U.S. officials recognize that, certainly after the flood, they are stretched too thin, that they probably couldn’t do it.

When I talked to Pakistani commanders in this zone, in Peshawar and outside, they basically said, don’t expect us to clear North Waziristan this year or probably even next year.

And I think the frustration for the U.S. is, basically, we’re looking at this porous border. The Haqqani Network, really one of the most bloodthirsty, in our view, factions of the Taliban, streaming in, I think General Petraeus is saying that…

MARGARET WARNER: Into Afghanistan.

DAVID IGNATIUS: Into Afghanistan. And General Petraeus is saying to the Pakistanis, either you do this, or we will do this.

We don’t really have the forces to back that up. And so, in the end, it’s not being done. There’s tremendous frustration. I think U.S. commanders see the time ticking out on their mission in Afghanistan, knowing that, unless they close the safe havens, they have got trouble.

MARGARET WARNER: So, that brings up Afghanistan front and center. Do the two governments actually have different — a key difference in their aims there? What’s the end state they would like to see?

SHUJA NAWAZ: I think Pakistan, like most countries in the region, heard the president’s speech at West Point last year, and saw July 2011 as the date by which the American military would begin withdrawing.

And the speed is not clear. But that’s what they heard, and that’s what they are hedging their bets on. Clearly, they don’t see a military solution to the conflict in Afghanistan. Success will be defined by how quickly the Afghans take over the fight and how much reconciliation can bring back people like Haqqani or other elements of the Taliban.

MARGARET WARNER: But, I mean, Petraeus and Karzai are saying the same thing, essentially, that it has to be a political solution. So, what’s — what’s the friction point between Washington and Islamabad on the Afghan conflict?

DAVID IGNATIUS: The friction point is that — is that the Pakistani government would like to be the key broker of any deal that’s done with the Taliban.

And they feel now that they’re being excluded. They hear reports about the U.S., the Karzai government, the British, various people talking with elements of the Taliban.

I actually think there’s a little less going on than the news of the last week might suggest in terms of real progress. It’s in the U.S. interest, of course, for the Taliban to think that there are elements of the Taliban that are doing a secret deal, and that will sow division.

But the Pakistanis are very frustrated. They think they’re being cut out of something. And they’re saying, you have got to bring us in, because it won’t work otherwise.

MARGARET WARNER: You know, underlying, both in this report, this NSC document, and also in the Woodward book is of course the fundamental nervousness in Washington about the stability of the civilian government, given that Pakistan is a nuclear weapons state.

Do you think that’s well-founded?

SHUJA NAWAZ: I think there’s adequate evidence of the weakness of the civilian government. It’s been evident in the recent floods in Pakistan and the very poor and tardy response to that, and the fact that the military had to step in and even withdraw 70,000 troops from the borders in order to cope with that.

So, that has really upset the — the very delicate balance inside the country.

MARGARET WARNER: Between the military and the civilian government?

SHUJA NAWAZ: Exactly. And that’s something that the U.S. and Pakistan should be aware of, because Pakistan’s needs are now going to be enormous for a number of years to come. And rather than have this kind of Mexican standoff on attacks across the border and closing the — the supply route, they need to focus on where that aid is going to come from.

Pakistan will need the aid. The U.S. needs Pakistan to ensure stability in Afghanistan leading up to July 2011 and beyond.

MARGARET WARNER: But the real nightmare scenario is that neither military, nor civilian government in Pakistan can hold it together, and that these nuclear weapons can fall into other hands.

DAVID IGNATIUS: Yes.

MARGARET WARNER: Is — how nervous are the people you talk to about that?

DAVID IGNATIUS: I think the nervousness about the nuclear weapons falling into the hands of the Taliban is more something in the press than — I think that’s viewed…

MARGARET WARNER: So, that’s not driving this?

DAVID IGNATIUS: … as an unlikely scenario. This report that the White House just sent to Congress is stunningly frank about how badly things are going in Pakistan and Afghanistan. Reading the discussion, this issue of the civilian government, a weak civilian government vs. the military, you almost have the feeling that’s what’s happened — and the U.S. is — is really recognizing this — is a kind of soft military intervention.

The military is now the decisive force in just about everything. And this report basically says, that’s so. It doesn’t endorse it, but it accepts that it’s reality.

MARGARET WARNER: Yes, this very frank tone in this, as you said. David Ignatius, Shuja Nawaz, thank you.