Hunting the world's most wanted warlord: Joseph Kony

The following script is from "The Warlord" which aired on April 14, 2013. Lara Logan is the correspondent. Peter Klein and Jeff Newton, producers.

Very little is known about a sensitive mission being carried out by a hundred U.S. Special Operations troops deep in the jungles of central Africa. They've joined several thousand African soldiers in one of the biggest manhunts that's ever taken place. Their goal is to help kill or capture the world's most wanted warlord, Joseph Kony and destroy his army.

This mission is part of a broader U.S. effort to counter the emerging threat to America from the growth of terrorist networks across Africa.

Joseph Kony has been on a murderous rampage that has lasted almost three decades, killing thousands and building one of the biggest armies of child soldiers in history.

Kony started out in northern Uganda, but his campaign has spread to four countries and he's now operating in this vast, lawless area in the center of Africa.

Our story, which includes images you may find disturbing, begins in the Central African Republic, with an elite tracking team from the Ugandan military that's searching for Kony in some of the most remote jungle on Earth.

You don't have to spend much time here to understand why it's so hard to find Joseph Kony. It's as isolated and unforgiving as it gets. The undergrowth so thick, every step is a battle.

When our producer Jeff Newton joined this Ugandan "tracking team," they'd been searching for Kony and his army, called the Lord's Resistance Army, or LRA, for three months, tracking them the way you would an animal.

Lukumbo: Right now, we are searching for the enemy tracks.

Jeff Newtown: Footprints?

Lukumbo: Yes, the footmarks of the LRA.

Twenty-seven-year-old Lt. Kasim Lukumbo's sole mission for the past three years has been finding Kony and he's one of the Ugandan army's top trackers.

The footprints are the first sign they've seen of Kony's army in six days.

As they followed the trail, the soldiers whispered so as not to give away their positions.

After an hour they reached this stream, but the tracks disappeared into the water.

Jeff Newton: No LRA?

Ugandan soldier: "No LRA. Let's go back."

There were no Green Berets on this mission. They do go out on operations like this, but they prefer to stay in the background. Keeping a low profile is part of the U.S. strategy.

Kurt Crytzer: They're the lead. They've always been the lead. We're relatively new here. We've only been here just about a year. It's really an African problem. It's being handled by Africans.

Col. Kurt Crytzer, a veteran Green Beret of 23 years, flew with us over the seemingly endless jungle, where the area they're searching is as big as Texas.

He took command of the U.S. Special Operations mission here not long after President Obama decided to send in troops 18 months ago.

Kurt Crytzer: The environment is some of the most unforgiving on planet Earth. When you get to the jungle, 50 feet in you disappear.

Lara Logan: You're like a ghost.

Video courtesy of Ugandan Defense Press Unit, Republic of Uganda, ITN Source and Media Africa

Kurt Crytzer: You're like a ghost.

Joseph Kony was 26 when he disappeared into the jungle, more than 25 years ago. Since then, his army has wiped out entire villages and burned houses down with children inside. They're known for cutting off the ears and lips of innocent people as a way to terrify them into submission. And no one has suffered more than the children -- the State Department says Kony's army has abducted more than 25 000. He turns the boys into killers, the girls into a harem of sex slaves and wives.

This video of Kony addressing his followers is one of the few times he's been filmed.

He's from a religious family in northern Uganda, an altar boy who became a witch doctor. When he started out, he wanted his Lord's Resistance Army to establish a government based on the Ten Commandments, but he's broken almost every one of them and his army is little more than a murderous cult.

Kurt Crytzer: Some things you just can't turn your-- a blind eye to, and I believe this is one case of that.

Lara Logan: The U.S. turned a blind eye to Joseph Kony for more than 20 years.

Kurt Crytzer: I can't account for why we did or why we didn't come. What I can tell you is we are here now.

Col. Crytzer and his men are the bridge between four African armies, who are working to find Kony and his fighters.

These soldiers are from the Central African Republic where many people believe Kony might be hiding. The Americans train them in their native French, using the language skills that come with being a Green Beret and they show them how to make the best of the little they have like using their beret as a field dressing or a stick as a makeshift tourniquet.

Col. Crytzer says they have to know how to treat themselves or they die.

Kurt Crytzer: Our guys bring support in small numbers. This is traditional advisory. This is something that looks like two American advisers out with 40 Ugandans on a tracking team. This is one guy going around throughout the villages building relationships.

Building relationships is central to the mission of Green Berets no matter where they are in the world. To earn the trust of the locals in these villages, Col. Crytzer's soldiers use their skills in unlikely ways - helping out at the local dentist and even delivering babies.

Together with diplomats from the State Department, they meet with the local tribes every day.

[SoF to villager: So I thank you very much for sharing the information with us helping provide the whereabouts of the LRA.]

They're trained to help and it's a chance to learn more about their targets.

Kurt Crytzer: If you think about our experiences with Osama bin Laden, we had some of the best platforms in the world flying in all the wrong places for eight years. In the end, it was human intelligence that led to him. In the end, it's gonna be human intelligence here that leads to Joseph Kony.

He told us some of the best human intelligence has come from those closest to Kony - like this man captured by Ugandan forces last year, Major General Caesar Acellam.

The Ugandan military granted us a rare interview with him. He's the highest-ranking LRA commander ever to be taken alive and knows more than almost anybody about what Kony's doing today.

Caesar Acellam: Kony is only struggling for survival.

Lara Logan: As Kony fights for his survival he's still killing people. He's still terrorizing villages.

Caesar Acellam: Yes, he's doing it.

Acellam - who claims he was abducted as a young man - spent 20 years with Kony and for much of that time he was his Chief of Intelligence.

We pressed him on the role he played in the countless atrocities carried out in Kony's name.

Lara Logan: You were part of an army that abducted children, that taught children to kill in a terrible way, to beat people to death, to crush their skulls, where young girls were raped. Did you witness that?

Caesar Acellam: I would say in a sense.

Lara Logan: Not in a sense. Yes or no?

Caesar Acellam: There were a number of things that you might not have wanted to do. But you do it. And all these people were doing atrocities, do it under Kony's instruction.

Lara Logan: Including you?

Caesar Acellam: Under Kony's instructions.

Lara Logan: Including you?

Caesar Acellam: Yes.

Acellam told us Kony rules by fear and claims he has mystical powers -- a formidable combination in the minds of children he kidnaps.

These young men were all soldiers in his army, rescued just a few months ago in the Central African Republic and brought home to northern Uganda. They were all younger than 13 when they were taken from their families.

Franklin: We were told this was God's war. So out of fear of God, I believed everything I was told, and I followed.

Franklin, Dennis and James all described a bizarre religious ceremony they had to undergo when they were initiated into Kony's army.

James: When you just arrive they smear some oil in the shape of a cross on your forehead here and on your chest and your back. And that's supposed to change you.

Lara Logan: Does it work?

James: Yes it works. It changes you completely.

Dennis; It numbs any thought you may have. It kills everything. You just listen to what Joseph Kony says.

And what Kony and his commanders told these young men to do - is almost beyond description.

Franklin: If a new abductee tries to escape, all of children were ordered to bite them to death.

Lara Logan: They would bite them with their teeth?

Franklin: Yes, until they died.

Betty Bigombe: They were robbed of their rights as children.

Lara Logan: And robbed of their innocence.

Betty Bigombe: Robbed of their innocence.

Betty Bigombe has spent more than two decades trying to help Uganda's child soldiers return to their families.

She told us this is what northern Uganda looked like just a few years ago - entire villages of children on the move, driven by fear and walking for miles to sleep in a place where Kony's army couldn't snatch them from their beds. For years they would do this every night, and return home in the morning.

Betty Bigombe: You look at these children and say they cannot feel secure to think I can sleep without thinking of anybody coming in to abduct or to kill them.

Lara Logan: Did you hate Kony for what he'd done?

Betty Bigombe: Oh, yes. Oh, yes.

Yet for many years, she's been the driving force behind the Ugandan government's efforts to make peace with Kony. When she first tried to contact him, he responded by sending her a message that was delivered in the most horrifying way.

Betty Bigombe: I was faced with five people. They'd been amputated and given letters to bring to me.

Lara Logan: Five people with their limbs hacked off with a letter for you that says what?

Betty Bigombe: They letter was all very bloody. The letter was saying that they were coming to kill me. I should stop mobilizing people against them.

Lara Logan: But that didn't put you off? That didn't stop you?

Betty Bigombe: No, if anything, it gave me even more determination.

Kony finally agreed to meet with her in 1994. To find him deep in the jungle, she says she had to walk for hours, escorted by his child soldiers.

Betty Bigombe: The speed at which they move in this jungles is amazing. They literally glide in. You see dust. And when he was coming, my God the drama.

Bigombe, who you see here, gave us this video of the meeting.

Betty Bigombe: His supporters were dressed like nuns. And then they were singing and then others would drop down, that the demon was coming. So many things happening at the same time and of course you look at this: "My God, where am I? What's going on in here?" Now when I'm seeing him sitting right there, I'm thinking, "I wish I could just open his brain and understand why he does what he does."

Bigombe left that meeting without a peace deal and today, the U.S. is pouring millions into getting Kony's soldiers to give up. Caesar Acellam who once stood at Kony's side, is at the center of that effort, working with the very enemy he once fought.

He's hoping for amnesty and is now the face -- and the voice -- of this campaign, recording messages that are then broadcast over areas of the jungle where Kony's soldiers are believed to be hiding.

And when Col. Crytzer's men hand out leaflets to the villagers to distribute in the jungle, it's Acellam's face they see.

Kurt Crytzer: You have a picture of Caesar Acellam on there. That's pretty powerful.

Lara Logan: So the idea is if members of the LRA see someone who was as senior as Ceasar Acellam and he's safe and well that that will convince people that there's a safe way out of this?

Kurt Crytzer: That's correct.

Col. Crytzer says he knows its working because Kony's soldiers have been defecting in increasing numbers, and his army is down to just a few hundred men.

Recently the Ugandans and the Americans temporarily suspended their hunt in the Central African Republic, because of political unrest, but not before Ugandan soldiers killed Kony's chief bodyguard close to where we filmed them; a sign that Joseph Kony's days may finally be numbered.

Lara Logan: How has one man been able to evade so many forces for so long?

Kurt Crytzer: He's a survivor. He's not an admirable human being, but he's an admirable adversary.

Lara Logan: Do you think you and the Ugandans are getting closer to Kony?

Kurt Crytzer: I believe we are. I can now wake up in the morning honestly and say, "Is today the day?"