ABC News Senior Foreign Affairs Correspondent Martha Raddatz was the first journalist to travel with the top U.S. commander in Afghanistan, Gen. John Allen, and other top generals since the killing of a half a dozen American soldiers following the inadvertent burning of the Korans on a U.S. military base. Raddatz was also the first reporter to travel with General Allen on a battlefield circulation.

Martha's exclusive television interview with General Allen aired Monday, March 5 on "ABC World News with Diane Sawyer."

Below is a transcript of their conversation:

ABC's Martha Raddatz: First of all I want to say through all of today, I never heard the Koran mentioned, which was pretty incredible.

General John Allen: Right, it's because of the relationship. There is a relationship here in this country at a personal level that most people don't have any understanding of … and that relationship can withstand shocks from time to time and it's the shock of combat right up close, it's the shock of something like the Koran. We apologized very early on and we asked for forgiveness and I think the nature of the relationship and the sense of trust is so great that they were willing to do that.

Raddatz: You know there's still some criticism in the country about that apology…

Gen. Allen: Why wouldn't we? Why wouldn't we? This is the central word of God for them, why wouldn't we? We didn't do it on purpose, but we should apologize, and we did, and moved past it, and I think that permitted us to move past it, because the apologies were sincere and the people recognized it and the relationships are strong and now we get on with the relationship, get on with the campaign.

Raddatz: And those apologies saved lives…

Gen. Allen: I think so. I think they did.

Raddatz: And just a couple quick more question about that and then I'd rather talk about the country as a whole, in terms of the investigation, can you talk about that at all?

Gen. Allen: I'd prefer not to, at this point, we're still working it.

Raddatz: But are you confident that it was inadvertent?

Gen. Allen: Oh, I don't think for a second that anyone intended to defame the religious publications or the Koran or anyone sought to desecrate the faith. I don't believe that for a second.

Raddatz: And you heard some Afghan officials who think it… who are also conducting investigations for Karzai, that they think it wasn't inadvertent, it was on purpose…

Gen. Allen: Well I can't, I can't help that. So, we're just going to push on with the investigation, investigations get to truth, you fix things that are broken and you hold people accountable; that's why you do investigations and we're headed in that direction.

Raddatz: And in terms of the country going forward, this is a very important year. I know we were out the other day with General Volesky and one of the things he said is that the Taliban are actually saying this is the year of the fight, this is a really big year for everybody, right?

Gen. Allen: Well, one of the disadvantages the Taliban will face this year in ways they didn't in years before is they fought from interior lines, they fought from inside the population, they're not inside the population anymore because last year they were rejected. Though another year of being rejected by the population and being rejected by the security forces to include now, increasingly, their own security forces, it's going to be it for them. We just had 50 Taliban reconcile down in Kandahar, and one of the points that they made is that when they were only fighting foreigners they had a purpose, they had a cohesion;  now when they take on security forces it has an Afghan face on it. Those Afghan faces are fighting and they know what to do, and that's bad news for them and 50 of them decided, "I don't want to fight my own people," especially when they're so capable.

Raddatz: And yet - and I said this in October, too - you have the largest amount of forces you're going to have and you do right now and the rest of the year you're going to see them draw down.

Gen. Allen: Sure. But it's not just an absolute departure.  First of all, the security force assistants, the advisers, all those young Marines I was talking to, those are the ones as individuals who are going to make such a huge difference here. But also the ANSF are stepping forward, by the thousands and thousands, and we've learned two things. First of all, we've learned that when they do step forward, they're better than we thought. The other thing we learned is, they're better than they thought! That's a happy dilemma, and when you put the right kinds of advisers in those formations, I'm confident. And, yes, there are fewer coalition forces, but with the numbers of ANSF online, and with the success of the advisory effort, we're going to be fine.

Raddatz: One of the things I heard today from the Afghan officials is that there is concern in the population, they hear drawdown, they hear 2014 everybody out, which I don't think is true, and it worries them.

Gen. Allen: Well the message I have is that this campaign, this relationship, is so deep and has been so important to us that in the context of a partnership or a strategic relationship our intent is to be here in some form for a long time. We don't know the numbers, and we don't know what we'll do in terms of the specific mission, but it almost certainly will be to continue the professionalization of the afghan national security forces, and we expect to do that for some period of time

[ BREAK ]

Raddatz: General, just the tail end of … finish this Koran burning stuff, do you think this is over now?

Gen. Allen: Well, we hope it is, we hope it is. This relationship is very strong, and we think that the strength of the relationship will carry us through this, and then on to the long-term future that we have together. So we hope it is, I think the sense of the President (Karzai) is that they want to move on…

Raddatz: President Karzai…

Gen. Allen: … President Karzai, the Ulema council, to want to move on. You've been with us today down in some of the hardest areas in Afghanistan, and people certainly want to move on and they stepped up to protect us when the time came, when there were voices being raised up against us. I think that we want to move on and I think the people want to move on, so, we'll see.

Raddatz: One final point is that I think looking at statistics the green-on-blue violence has been getting worse, and obviously we've got a lot more troops now, does that concern you?

Gen. Allen: Sure, it's another dimension of force protection that we're looking at very very closely. We're working closely with the Afghan government, the minister of defense, the national director of security; they're operating in ways we haven't seen in a very, very long time, and it's creating unprecedented opportunities for them to come together and try to solve this as well. It's important to note that the green-on-blue, or what we call the insider threat, isn't just oriented on us, the Afghans have suffered nearly as many casualties as we have in that regard. So it isn't just about us,  and it isn't just about the Taliban. I've said, said in other places that the Taliban take credit for everything, they don't have to tell the truth . (inaudible) But the truth is, many of these folks are self-radicalized, or they've got a problem that exceeds their ability to continue to deal with it,  and so it isn't just about the Taliban, in fact it isn't mostly about the Taliban, and that's an important thing for people to understand. It's an important thing for us to keep in mind, and it's an important thing for people to understand when they seek to grip the issue of the green-on-blue.

Raddatz: Let me just talk in a personal sense for you what these last couple of weeks have been like. I mean, you had to wake up that morning and think, "This is going to be bad."

Gen. Allen: Well, as a strategic commander you seek to grip the campaign and keep it on track (inaudible) you work closely with your civilian and diplomatic counterparts, and there are going to be those occasions, and I talk about it from time to time, where you're going to take a body blow. Which you've got to reach down inside, grab those things that give you your sense of spiritual orientation, and push on. As I told my folks, my commanders that morning, keep your eyes on the horizon, understand the strength of the campaign, and don't let this come off track. You know, great powers don't get angry, great powers don't make decisions hastily in a crisis. We've got a good campaign, we've got a good relationship, we keep our eyes on the horizon, we grip the campaign, and we move on. It's been challenging, but we're going to get through this.

Raddatz: It did kind of rip your heart out when the interior ministry shooting happened.

Gen. Allen: It was very sad. It was very sad indeed. And I was heartened, if there was any way to be encouraged by the grief, by the outpouring of grief by the members of the ministry of interior as well. So it wasn't for them just an isolated event, for us it certainly wasn't, it was a great tragedy, but for them it was just as tragic. And they went to great lengths to explain to me that they felt as though a member of their own family had been killed, their two young officers had been killed in their own home, which for Afghans who are famous around the world for hospitality, this was for them a great tragedy, and their outpouring of grief, and their outpouring of condolence to us was genuine and continues to this day.

Raddatz: One last question, what would you like Americans to know they're losing sight of, I guess?

Gen. Allen: I don't know exactly on those issues Americans are sighted today, but I would simply tell them we remain oriented on the mission, and I would simply tell them that every single one of their sons and daughters over here is working around the clock to accomplish this mission on behalf of the United States and on the behalf of the Afghan people and we really believe in this mission. I'd ask them to keep that in mind as they think of us every single day (we're) over here.