"Insider attacks" kill U.S. troops in Afghanistan

Eleven years after 9/11, Lara Logan talks to the top U.S. commander in Afghanistan, Gen. John Allen, who is incensed over deadly attacks on his men by Afghan troops the U.S. has trained and supported. In this hard look at the Afghanistan war, she also talks to President Hamid Karzai and a Taliban commander.

The following is a script from "The Longest War" which aired on Sept. 30, 2012. Lara Logan is the correspondent. Max McClellan, producer.

The war in Afghanistan is now the longest war in American history. Eleven years after 9/11, the enemy the U.S. went there to defeat, is coming back, according to the two men who know more about this than anyone: U.S. General John Allen and Afghan President Hamid Karzai.

We interviewed both of them, and they were blunt about where the war stands and about an enemy tactic that's killing more and more Americans.

We arrived in the Afghan capital just after four U.S. soldiers were gunned down by an Afghan policeman who was with them in a firefight. It's what the U.S. military calls an "insider attack" when U.S. forces are killed by the Afghans they're training and fighting with. Last month, these attacks were the leading killer of American troops.

It's a critical problem for Gen. Allen, whose job is to make sure Afghan security forces take over the fight so U.S. soldiers can come home.

Lara Logan: You're in a tough spot right now. Can you explain why the sudden increase in these attacks?

Allen: Well, I'm mad as hell about them, to be honest with you. We're going to get after this. It reverberates everywhere, across the United States. You know, we're willing to sacrifice a lot for this campaign. But we're not willing to be murdered for it.

Lara Logan: At a certain point, if these attacks continue, the American people are going to say, "We've had enough." Right? "Why are we training these people if they're murdering us?"

Allen: Well, that may be, in fact. It may be the voice right now that we're hearing. The key point is for us to understand that the vast majority, the vast majority of the Afghans, and you've lived with them, you understand these people, they're with us in this. They understand right now the severity of this problem and the urgency of what's happening. And there have been Afghans who've been killed trying to save our forces when these attacks have been underway. Because that was the only reaction that they could've taken, was to try to save us at that moment of attack.

Training Afghan troops, like these Afghan Special Forces soldiers, is the centerpiece of Allen's mission. He's already had to suspend training twice because of the rise in insider attacks, which are threatening America's exit strategy.

Lara Logan: Should Americans brace themselves for more attacks? Is this going to continue?

Allen: It will. The enemy recognizes this is a vulnerability. You know, in Iraq, the signature weapon system that we hadn't seen before was the IED. We had to adjust to that. Here, I think the signature attack that we're beginning to see the-- is going to be the insider attack.

Allen has asked Afghanistan's president, Hamid Karzai, to do something to keep enemy elements out of the Afghan army and police.

Karzai: These attacks are sad. This is something I have discussed in detail, something that I bear responsibility for, to correct.

We met Karzai at the presidential palace in Kabul where he spends most of his time. He rarely ventures beyond these manicured grounds and fortress walls that have housed Afghanistan's leaders for more than a hundred years.

And with good reason: he's survived four serious assassination attempts, like this one in southern Afghanistan in 2002 when U.S. Navy SEALs guarding him gunned down his attacker.

Now, as his forces take over security, they still face a formidable enemy.

Lara Logan: Can you tell Americans what's still at stake in Afghanistan after all these years of war?

Karzai: The reason for the NATO and American intervention in Afghanistan was terrorism. Terrorism has not gone away. It has increased.

Lara Logan: When you say that terrorism has increased what do you mean exactly?

Karzai: If terrorism means violence against civilians, if terrorism means violence against our allies. It has increased. It has not abated. It has not gone away.

Karzai says Afghan intelligence reports to him on the presence of foreign fighters - Arabs, Chechens and others, who are captured and killed on Afghan soil.

Karzai: Name them al Qaeda, name them Islamic Movement of Uzbekistan, name them Haqqani, name them Taliban, whatever. They're still there. And they have the ability to continue 10 years on to come and hurt us and kill your troops and kill our troops, kill our civilians. We must then question how come they've returned?

Lara Logan: Well that's a good question. How come?

Karzai: How come they've returned?

Lara Logan: How did that happen?

Karzai: Something must have gone wrong for that to happen.

One place where things have gone wrong is in the mountains of Kunar in the east of the country, which has become al Qaeda's base of operations in Afghanistan today.

These are enemy fighters and leaders filmed there by our Afghan cameraman who visited a number of different enemy camps. We couldn't go ourselves because it's too dangerous for Westerners to travel on their own to Kunar. They told our cameraman that they work side-by-side with al Qaeda and share their ideology.

One Taliban commander agreed to meet with us in the Afghan capital. He's a specialist in suicide bombings trained by al Qaeda. The safest place we could find was the back of a car, and he would only talk if we concealed his identity.

As we made our way through the streets, we had to avoid the city's heavy security and keep our cameras hidden from view.

Lara Logan: Who is behind the "insider attacks", what the Americans call 'insider attacks,' infiltrating the Afghan police and army - is that you?

Taliban: These are Taliban attacks. This is part of our new military strategy. We have our people in the Afghan police and the army. And the orders come from the top.

He told us al Qaeda fighters are rushing to Afghanistan and that he has more than a dozen of them under his command. He also said they have been the driving force that has made the Taliban more lethal on the battlefield.

Lara Logan: Are you the only commander with al Qaeda fighters?

Taliban: There are many groups that have them. We can't do this without them.

Lara Logan: What skills do the al Qaeda fighters bring?

Taliban: They are masters of everything. For example, making IEDs, something we don't know how to do. But they are teaching us. They are also master engineers and good with all weapons. When our weapons break, they are the ones who repair them. We can't do this without them.

While the U.S. has been saying for a long time that al Qaeda in Afghanistan is almost defeated, the U.S. military's own reports from the battlefield reveal a very different picture.

They are rich with detail about al Qaeda's leaders and operations today, confirming the existence of al Qaeda training camps and multiple attack cells. Among those they say they've killed are al Qaeda weapons and explosives experts. In one month, the U.S. says it killed more than 25 al Qaeda leaders and fighters.

Allen: Al Qaeda has come back. Al Qaeda is a resilient organization. But they're not here in large numbers. But al Qaeda doesn't have to be anywhere in large numbers.

Lara Logan: Right, the numbers are not significant.

Allen: They're not significant in a traditional military sense. Al Qaeda has significance beyond its numbers, frankly. And so for us, our 24-hour-a-day objective is to seek out those al Qaeda cells. And, as we seek them out, to target them and eliminate them. And we're doing that 24 hours a day. We do not want al Qaeda to feel as though it can put down roots here. That's the key.

A four-star general like Allen is expected to be as much a politician as a warrior - and one of his more sensitive tasks is dealing with the Afghan president whose relationship with the U.S. has soured in recent years. We found the president frustrated with the ongoing bloodshed.

Karzai: A lot of innocent people die every day, the question is what have we done wrong that they are still able to continue to hurt and damage people? That is for me as the president of Afghanistan the most important question. And that is the question that I've engaged with the United States almost daily.

Lara Logan: And are you satisfied with the answers you get from them?

Karzai: Never. No. Never. That's been one of our difficulties.

Not satisfied, Karzai told us, with the answers he's getting from Allen.

Karzai: I have letters from Gen. Allen who says that the security in Afghanistan is a lot better and the people are waiting for improved governance.

Lara Logan: Do you agree with him?

Karzai: I - No, I don't agree with that.

Lara Logan: You tell him that?

Karzai: Yes.

Lara Logan: What does he say?

Karzai: The security has improved but not - not completely.

Lara Logan: He doesn't agree with that. He says that's wrong. And he's told you he's not satisfied with the answers he's getting from you. What do you say to that?

Allen: Well-- (LAUGH) I think we have a difference of opinion on that. The security situation isn't perfect around the country. I mean, there are lots of areas that remain insecure probably is the word. But an awful lot of the population of this country is living in an area where there is vastly improved security from where it was just a few years ago.

They did agree on a few things. Right now there's no peace process at all with the Taliban and Pakistan is the problem. Enemy fighters from the Afghan battlefield have enjoyed freedom and sanctuary on Pakistani soil since the beginning of the war.

Lara Logan: Ultimately, it's not going to matter what you do if you do not address the critical element of the safe havens that the enemy has inside Pakistan, across the border, in many ways, out of your reach.

Allen: Well, we're doing a great deal right now. The relationship that we have between ISAF forces and the Pakistani military has improved dramatically--

Lara Logan: But it doesn't stop Pakistanis helping our enemies kill U.S. soldiers.

Allen: Well, that's not going to stop immediately. We've got to work at that. It's not a solution that can be had ultimately by a military solution. These are policy issues, these are government to government issues. I'm not going to be able to wage war in Pakistan. But this is hard. There's a very complex relationship with Pakistan. And we'll work very hard and very closely with the Pakistani military to achieve common objectives. But to some extent the Pakistani military has been successful in cooperating with us in the last several months with regard to complimentary operations on both sides of the border but much more needs to be done.

Lara Logan: Your deadliest enemies on the Afghan battlefield have complete freedom of movement inside Pakistan with the blessing of the Pakistanis. And every commander that's sat in your shoes has had to try and build a relationship and go through the same motions time and time again and the effect on the battlefield remains exactly the same. American soldiers continue to die because of the support Pakistan gives to America's enemies.

Allen: You've just stated the truth.

Lara Logan: That's got to make you mad.

Allen: Yes, it does. Yes, it does. And within the context of my authorities, we're going to do everything we can to hunt down and kill every one of those Haqqani operatives that we can inside this country. And those other elements that come out of those safe havens that ultimately threaten my troops, threaten the Afghan troops and the Afghan society, the Afghan civilians, and ultimately the Afghan government.

Karzai blames the U.S. for not confronting Pakistan years ago.

Lara Logan: Why has the U.S. failed to address the issue with Pakistan do you think?

Karzai: Perhaps politics.

Lara Logan: What has been the cost of that?

Karzai: Heavy for us. Disastrous for us.

Lara Logan: Would Afghanistan look completely different today if the issue of sanctuary and safe haven in Pakistan had been dealt with years ago?

Karzai: Absolutely. Completely different. Much more peaceful. Much more progressed. Much more stable. And a society that would have been thriving on its own.

Lara Logan: Does that make you angry?

Karzai: Absolutely. Very much. And we have shown it.

Lara Logan: Was there much yelling and screaming behind closed doors?

Karzai: Plenty of that.

Lara Logan: Listening to you I get the feeling that there's a lot of anger towards the United States. There's been bad blood. What went wrong? Why do you feel this way?

Karzai: I don't feel angry. I'm -- Afghanistan feels let down.

Karzai has repeatedly expressed his gratitude for the sacrifices the U.S. has made in his country, but in recent years he's been outspoken and critical of his American partners.

Lara Logan: When Americans hear you criticize the U.S. they think of all the taxpayer money that they have sent to Afghanistan and the American lives that have been lost here. And some question what kind of partner you have been.

Karzai: So-- our criticism is not directed at the American people. Our criticism is directed at policies and behavior of those who are representing the United States people - and is in a manner of asking for change and improvement.

Allen knows that America's combat mission in Afghanistan is drawing to a close. He told us he expects they'll be fighting to the last day of this military campaign which began with 9/11...and will end -- the White House says -- 27 months from now.

Lara Logan: How do you feel about having a political timetable for your military campaign?

Allen: Well, it focuses us pretty good. Yea. I walk home at night after a day here and with 27 months on the clock, I ask myself every night whether I've done enough and some nights I turn around and go back.

Lara Logan: I get the feeling sitting here talking to you, listening to you, that this is not just a job. It's not about the next promotion. You're carrying this campaign in your heart--

Allen: Yeah--

Lara Logan: --this matters.

Allen: Yes I am. I came here believing this would be the last job I'd ever have. I don't care about anything beyond this. This is what's important to me. I almost can't remember ever having been anywhere else. This is completely consuming for me. And I am dedicated 24 hours a day to these magnificent troops, to the Afghans, to this cause, and ultimately to the successful completion. This is very personal to me. And I take it very personally.