The following script is from "The Killing Machine" which aired on May 8, 2016. Lara Logan is the correspondent. Max McClellan and Richard Butler, producer.

American soldiers have been drawn deeper into the war against ISIS and this past week a third U.S. serviceman was killed in northern Iraq. It's a fight that began more than a year and a half ago when ISIS was expanding it's territory and it's been hard to shed light on the areas under its control because most reporters can't go there. But there have been some places where ISIS has been run off, and Sinjar is one of them.

Displaced Yezidis flee violence in Sinjar Reuters

It's a small city that lies on a highway connecting ISIS territory in Syria to its territory inside Iraq and when ISIS fighters took control they began to systematically wipe out the Yezidi peoplewho lived there.

After Sinjar was liberated, we went there with Father Patrick Desbois, a French Catholic Priest, who is one of the world's leading voices on genocide. He spent 15 years documenting the mass murder of Jews by Hitler's mobile death squads. Now he says he's on a mission to expose what he calls the ISIS killing machine.

This is what is left of the ancient Yezidi city of Sinjar. We put a camera on a drone to try to capture the enormity of the devastation. ISIS sees the Yezidis as devil worshippers and their policy here was total annihilation. What you're looking at is a thousand years of civilization reduced to rubble in 15 months of terror.

Last November, some 7,000 Kurdish Peshmerga soldiers backed by heavy U.S. airpower, pushed the Islamic State out of here. The Kurds said they killed around 300 terrorists in the two day offensive.

This is what it takes to claim a city back from the Islamic State. There is nothing left. Any direction you walk, all you find is more destruction. One street after another, an entire city literally in ruins.

We walked the shattered streets of the Yezidi heartland with Father Patrick Desbois, who was on his fourth trip to Iraq. He told us what ISIS didn't destroy, Kurdish forces leveled as they fought their way in.

Father Desbois: I asked the Peshmerga, they told me it was the only way to make ISIS go, the only way to make them go is to destroy the city.

Lara Logan: The only way to defeat them?

Father Desbois: Yea, it's terrible.

Father Desbois has been studying the minds and methods of mass murderers like Hitler most of his life and he'd come here to investigate the genocide of the Yezidis by ISIS, an organization more sophisticated than he expected.

Father Patrick Desbois CBS News

Father Desbois: It's not easy to manage your war, to manage international terrorism and to manage a genocide in same territory. Hitler, it took for him a long time before doing all that. And ISIS they did it so quickly.

Lara Logan: Does that speed frighten you?

Father Desbois: Yeah, it's frightening because it means actually there is a kind of science of terrorist, war and genocide. They developed a science.

The Islamic State stormed into Sinjar in August 2014. They murdered at least 5,000 and kidnapped thousands of others as they cleansed the land of Yezidis.

Father Desbois said their strategy here was unlike anywhere else. Those who could fled to Sinjar Mountain, where images of their desperation reached the world, in part prompting the first U.S. airstrikes of the war.

Evidence of the ISIS killing machine lies, Father Desbois said, in the city's remains.

Lara Logan: Which building is this?

Father Desbois: It's where they put the Yezidis - (all the Yezidis of Shingal)

That's why he brought us to what's left of the main Administration building.

Father Desbois: That is the beginning of genocide, it's the first step for me.

Lara Logan: In this building.

Father Desbois: Yea.

Here, ISIS rounded up Yezidi men, women and children.

Father Debois: They say to people, "Don't worry, we'll bring you to a nice building." It's why they accept.

Lara Logan: And they don't think that they're going to die?

Father Debois: No.

Lara Logan: That's why they come?

Father Debois: Yeah, that's why they come. And here begins the selection. And so this system is system of permanent, permanent selection.

Father Desbois said they're registered, separated and ordered to hand over money, jewelry, cellphones. ISIS had a plan for everyone.

Father Desbois: They see a boy who is 10 years old, he can carry a bomb, he will carry bombs. They see a girl, she's beautiful. Oh, she will be sold to an Emir to be a sex slave. They have the sense of utility. A person is only to be used for something.

Lara Logan: So each person has a purpose?

Father Desbois: Each person has a purpose.

Lara Logan: And if they have no purpose, what happens?

Father Desbois: They kill them.

Wherever we went in Sinjar, Kurdish soldiers came with us. They said there were still hidden bombs all over the city and Father Desbois used them as a guide.

Lara Logan: So where are you/they taking us? The tunnels?

Father Desbois: Over to one of the tunnels. Yea.

ISIS owned this ground for 15 months, transforming Sinjar into a fortress with tunnels underneath the city. The entrance to one was inside this house.

With ISIS still around two miles from here, the soldiers were tense. What we found, surprised us...

Lara Logan: That's incredible. I mean it just looks like a normal house.

There were mountains of dirt in every room. Whatever they took from the ground, they kept inside these walls, so American drones wouldn't see a tunnel being built.

This particular tunnel goes to the home of the Islamic State emir of the city, basically the top guy in charge here when the Islamic State was in control. And we're told that he and his inner circle - his bodyguards, his men - would hide underground here with him during the bombings.

Out on the street, Father Desbois was approached by survivors, desperate for answers about family members still missing.

[Father Desbois: What was the name of his father?]

There are mass graves across Sinjar and we had been to some of them. At this one east of the city where Kurdish officials had marked off the site, there were human bones still scattered in the dirt. It's believed Yezidis fleeing to Sinjar Mountain were caught by ISIS and killed here.

Lara Logan: It's impossible to know how long it's been here?

Father Desbois: No, we don't know. Only a doctor can say.

And in this mass grave on the outskirts of Sinjar, he was told some 80 Yezidi women were executed.

Lara Logan: They shot them right here?

Father Desbois: Yeah.

Lara Logan: And how do they know this?

Father Desbois: We know this because-- we can find bones and everything underground.

Lara Logan: There's half a skull there and two skulls there?

Father Desbois: Yeah. And here you half of the head. And here, too. It's really a shooting, extermination site.

At every site we visited, his team photographed and filmed the evidence and recorded GPS coordinates so they could come back. His lead investigator, Nastasie Costel, has been at his side helping to locate killing fields like these for years.

As they carry out their investigation in Yezidi towns and villages, Father Desbois is not asking eyewitnesses to recall what they saw more than 70 years ago, like he did with the Holocaust.

Father Desbois: How many people are buried here?

This time, he's interviewing survivors with the horror still fresh in their minds.

Lara Logan: So how does that change your investigation?

Father Desbois: It's completely different because the challenge now is to stop the genocide, is to try to save people, is to try to carry the voice of the victim, to make people conscious. The killing machine is alive.

Lara Logan: So, do you feel a sense of urgency then?

Father Desbois: Urgency and the immense tragedy also to have the conscience that the world doesn't wake up more now than '42.

For the Yezidis, there is no holier place than the temple of Lalish, about a hundred miles from Sinjar. They believe in one god and seven angels, an ancient religion that over time has adopted elements of many faiths.

Lara Logan: As long as they have been on earth, the Yezidis have been persecuted. Why do you think that is? They are peaceful people.

Father Desbois: Yeah, it's a people who, as I understand refuse to assimilate and so it was like a pocket of resistance inside the Islamic world.

Their faith is passed orally from generation to generation. So they have no sacred written book like the Bible or the Koran, which is one of the reasons ISIS has condemned them to death or sexual slavery. When Yezidi women are rescued or escape from the Islamic State they come here to the spring that flows under the temple to be cleansed.

Now the Yezidis are landless in their own land. There are nearly 200,000 living in refugee camps about 120 miles northeast of Sinjar in Kurdistan, where Father Desbois spends most of his time...piecing together a picture of what happened to the Yezidis of Sinjar.

He's recorded over 400 hours of testimony so far more than 80 men and women, much of which we caution you is disturbing to see and difficult to hear.

[Testimony: They burned him completely from his feet until to his head.]

And he allowed us to sit in with him on his second interview with Nasreen, who is 21. Still terrified of ISIS after more than a year under their control, she covered her face.

The wife would hold down my hands as the husband raped me, she told Father Desbois. She said at one point, she was tied to a bed, naked for three months, and raped...day and night.

Father Desbois: It was many men every night?

Nasreen: Everyday there would be ten men and they were from all countries.

Maha is 28. She had recently arrived in the camp, held by ISIS or Daesh as they're known here, for almost a year and a half. She gave these photographs to Father Desbois, which she said ISIS had taken. They showed three of her children dead, poisoned, she claimed, by the man who was raping her. He killed them because we tried to escape, she said.

But for Father Desbois, the heart of the ISIS war machine is not only the suffering of the Yezidi girls.

Father Desbois: If we show only the girls I think in one way, the Daesh, they don't care. It's not very secret. Very secret is the long-term machine they are preparing. I'm afraid that they use the image we give of them, rapists, it's like if you say Hitler was a rapist. Say, yes, they raped a lot of girls. But unfortunately it was a much larger machine and ISIS is the same category of machine.

Lara Logan: Very little is known about that.

Father Desbois: Very little. Very little. And for me, that's the secret of Daesh.

A secret that lies with boys like these two brothers who for their safety asked us not to use their names. They said ISIS kept them alive to train them as terrorists.

Brothers who say ISIS kept them alive to train them as terrorists CBS News

"Everything they did was to try to make us like them," he said. "They ordered us to plant hundreds of bombs and taught us how to detonate them."

Father Desbois: It seems a person received a bullet in the head...

Forensic specialists are finally beginning to exhume these mass graves and the number of dead -- already around 5,000 -- is expected to rise. As the Yezidi genocide enters its 21st month, there are still about 3,000 Yezidis being held by ISIS today.

Lara Logan: How do you stop the machine?

Father Desbois: It can be stopped only military.

Lara Logan: Militarily.

Father Desbois: Only military. I-- how-- how could be-- be stopped Hitler?

Lara Logan: You had to defeat him on the battlefield.

Father Desbois: In one way or another.

Lara Logan: And kill the idea.

Father Desbois: And kill the people who carry them.