>> NARRATOR: Tonight on Frontline.

>> RAMITA NAVAI: The only way to get in and find out what's really happening is to go in undercover.

>> NARRATOR: Correspondent Ramita Navai is on the ground in Iraq.

>> NAVAI: Last year, two Iraqi journalists investigating the militias here were murdered.

>> NARRATOR: Investigating Shia militias... (explosion) ...as they help drive ISIS out of the country.

>> NAVAI: While the West is fighting the war against ISIS, most people we've spoken to here told us they're much more scared of the militias.

>> (men shouting) >> Many people in the government feel that they are powerless to do anything.

>> NARRATOR: Tonight, "Iraq Uncovered."

Tonight's program contains violent and graphic imagery.

Viewer discretion is advised.

(chatter on radio) >> RAMITA NAVAI: I'm traveling through northern Iraq, heading to the district of Al Fat-hah.

Until recently, this was ISIS-held territory.

We've been driving for a few miles north of the country and every now and again we come across a scene like this.

This is the town of Beji.

I should say it was the town of Beji, just look at it.

I'm on my way to meet a militia fighting against ISIS.

With the world's attention focused on the battle in Mosul, this is one of the war's hidden fronts.

Few journalists come here.

You can see how close we are to ISIS now.

On both sides of the road you can see black smoke billowing out, and that's from oil wells that ISIS have set on fire.

This unit has advanced deep into ISIS territory.

Alongside the Iraqi Army, militias like this have played a critical role in driving back ISIS across Iraq.

I want to find out how they operate.

And how far are they?

>> NAVAI: They're pointing over there and they're saying, that's the black flag of ISIS.

And there it is.

These militiamen are Shia Muslims, like 60% of Iraqis.

There are over 40 Shia militia groups in Iraq with about a hundred thousand fighters.

Most of them joined in 2014 in response to the rise of ISIS.

How many men have you lost here?

>> NAVAI: These men are in the Badr Organization, the biggest militia in Iraq.

Last year, along with other militias, they were granted official recognition by the Iraqi government.

They are supposed to answer directly to the prime minister, but in practice they have their own allegiances and chains of command.

The post's senior officer, who goes by Abu Sajjad, says ISIS attacked a few days earlier.

>> NAVAI: The bodies of ISIS fighters lie between the lines.

(shouting) Suddenly, the militiamen spot some civilians fleeing ISIS territory.

We head into no-man's land to meet them.

The road is pockmarked with craters from IEDs that ISIS fighters plant every night.

The family's right ahead of us, a few dozen people.

They've been walking all night to get here.

Salam Alaikum.

The refugees are Sunni Muslims, from the ISIS-held town of Hawija.

How are you feeling, how was your journey?

(baby crying) >> NAVAI: The guys here say we may be monitored by ISIS right now, fighters often shoot across, so we're leaving.

>> NAVAI: The militiamen bring the refugees to their base for screening.

How did you escape?

>> NAVAI: Today they've escaped ISIS but now they face a new ordeal.

The militia separate the men from their families.

ISIS follow their own violent version of Sunni Islam, so the Shia militia often see Sunni refugees as ISIS suspects.

And in this part of Iraq most people are Sunnis.

>> NAVAI: What are the chances that you've got some ISIS fighters in that room?

>> NAVAI: But it's such a hard process to really tell if somebody is an ordinary guy or if he's an ISIS fighter.

How can you be 100% sure?

(shouting) >> NAVAI: So the guys just pulled this man away.

They're telling me now that families here have said that he tried to blackmail them.

That when they were fleeing, he said if you don't pay me, if you don't give me money, I'm going to go and tell ISIS that you're fleeing and they'll kill you.

>> NAVAI: It's suddenly got quite chaotic here.

They're accusing him of being an ISIS fighter.

We weren't allowed to follow him.

We don't know where they've taken him.

One of the militia leaders takes us to a building where they're holding ISIS suspects.

As we approach the building, we keep filming with a phone.

The militiamen tell us the prisoners were picked up among refugees fleeing ISIS territory.

We don't see the man who was just arrested.

There are are over a hundred men in there they say are ISIS fighters, ISIS sympathizers.

The conditions are really cramped.

The men didn't look like they'd been beaten, they did look pretty terrified.

Under Iraqi law, ISIS suspects are supposed to be brought quickly before a judge.

But the militia fighters say some of these prisoners have been here for three months.

I speak to Badr's local head of intelligence, Sheikh Haidar.

Why aren't they in official prisons?

Why haven't you handed them over to the government?

>> NAVAI: To many Iraqis the militias are heroes, but human rights organizations claim some groups consistently mistreat Sunni civilians.

A number of Sunni politicians are investigating these allegations.

I head to Baghdad to meet them.

One is a member of parliament from the Sunni province of Anbar, Lekaa al Wardi.

>> NAVAI: She tells me that in summer 2016, a Shia militia group called the Hezbollah Brigades took away hundreds of Sunni men after driving ISIS out of a town called Saqlawiyah.

Leka has just given me these three documents.

And they list over 600 names of people Leka says are still missing.

>> NAVAI: How dangerous is it for you speaking out like this?

>> NAVAI: Online I can see the Hezbollah Brigades posted video of the battle for Saqlawiyah.

(shouting) It shows the town's Sunni residents celebrating liberation from ISIS.

But there's no mention of the over 600 Sunni men and boys I've been told are missing.

Saqlawiyah is 45 miles from Baghdad.

Hundreds of thousands of Sunnis have been displaced by the fighting in this area.

Many of the women from Saqlawiyah have fled to the Amriyat Al Fallujah refugee camp.

(women weeping) >> NAVAI: What do you think has happened to the men?

>> NAVAI: The women are saying that all these children here are missing their fathers.

An investigation by the local governor found that 643 men are missing, and that hundreds more were Sunni men were imprisoned.

We discover a man who says he was held captive hiding in the refugee camp.

As with others we meet, we agree to disguise his voice.

>> NAVAI: Officials say 49 of the imprisoned men died in custody.

(shouting) This local news footage shows other Saqlawiyah prisoners immediately after their release.

They also say that they were tortured.

>> NAVAI: Survivors say that some of the men who tortured them wore the badge of the Hezbollah Brigades.

>> NAVAI: Has this changed the way you feel about your country?

>> NAVAI: The Hezbollah Brigades fought U.S. troops during the American occupation and are on the State Department list of terrorist groups.

No one from that militia would talk to me.

Walking through this camp, dozens of people keep coming up to us telling us they have loved ones missing.

On top of that, people are still going missing.

Only a few days ago a handful of families tried to go back to Saqlawiyah and some of the men were taken by militias.

The Iraqi government has opened an investigation into the disappearances in Saqlawiyah, but hasn't released any findings.

I want to find out more about Saqlawiyah and other cases I've heard about.

So I contact the prime minister, who's been trying to gain greater control of the militias.

I also contact seven other senior officials in the government and military.

They either decline to be interviewed or don't get back to me.

However, one of Iraq's most prominent politicians, a Shia-- but a vocal critic of the militias-- agrees to talk to me.

>> They became too strong, politically at least for now, than the army and the police.

>> NAVAI: Ayad Allawi is one of three vice presidents, but opposes the government on many issues.

There's a government investigation into the disappearances at Saqlawiyah, but nobody I spoke to... >> There will be no answer.

>> NAVAI: So the government is not really interested?

>> No, no, it's dead, it's dead like other inquiries.

Nothing, nothing.

Any explosions, killings, intimidation, people disappearing in prisons, no inquiry whatsoever.

Nobody was taken to courts.

Nothing is happening.

>> NAVAI: And why?

Is it because the militias have more power?

>> Because they don't want.

Because powerful people are involved and there is a cover-up.

And they don't want realities to be divulged.

That's why we feel, and I feel, and many people, also, by the way, in the government feel that they are powerless to do anything.

>> NAVAI: Iraq's government is divided, and the vice president told me there is no concerted effort to control the militias.

I want to know more about how these groups are operating on the ground, so I head to a Shia militia stronghold: the province of Diyala.

Access to Diyala is tightly controlled, the province is pretty much run by the militias.

There are checkpoints everywhere, so the only way to get in and find out what's really happening is to go in undercover.

Parts of Diyala used to be under ISIS control, but they were driven out in 2015 by a coalition of Shia militias led by the Badr Organization.

I've been told life hasn't returned to normal.

Last year two Iraqi journalists investigating the militias here were murdered.

The journalists were killed outside Muqdadiya, the town I want to reach.

Muqdadiya is the heart of Shia militia power in Diyala province.

Even in villages there are checkpoints.

This is the second one that we've come to in this village.

We've got to put the phone down now.

I've arranged to secretly meet a disillusioned Shia militiaman willing to take me into Muqdadiya.

He's a member of the Badr Organization.

We've stopped on the side of the road.

He's said we need to get into his car.

You can see it in front.

It's unmarked.

He says it's known to all the militiamen in this area and that's the only safe way that we can get through checkpoints here.

>> NAVAI: He takes me into the center of Muqdadiya.

I can still see the signs of the battle against ISIS.

In this town, Shias and Sunnis live side by side.

The militia insider says some of his fellow militiamen have been taking revenge on the Sunni population for ISIS attacks.

So on my left here is a Sunni mosque.

You can see that it's been completely destroyed.

>> NAVAI: He takes me to another Sunni mosque.

I'm looking through the gates now and it's just a mound of rubble.

In all he shows me six destroyed Sunni mosques.

The militiaman claims a local imam even handed out lighters to his unit to burn Sunni homes.

>> NAVAI: The Iraqi government announced an investigation into the situation in Diyala more than a year ago, but it hasn't made any of its findings public.

The fighter says that although there are federal police in Diyala, they can't take on the militias.

>> NAVAI: He says he knows of Badr militiamen who have kidnapped and killed Sunni civilians with impunity.

Different militia groups have carved up the town and have also been accused of abusing Sunni civilians.

They've even started fighting for territory between themselves.

We've just had to turn around because the militiaman said that that area is too dangerous to enter.

>> NAVAI: He's worried we're attracting attention.

He takes us back out of town and leaves us.

I want to investigate the militiaman's claims.

Outside Muqdadiya, I meet a Sunni man who says militiamen recently kidnapped him and tortured him for a week.

>> NAVAI: He couldn't tell what militia they were from, and says he was only picked up because he's a Sunni.

>> NAVAI: When the kidnappers moved him to a different location, he claims the police turned a blind eye.

>> NAVAI: He tells me he knows 22 people who've been kidnapped, and that 17 are dead despite their families paying a ransom.

The numbers are impossible to verify, but human rights groups have documented widespread kidnapping and killing by militias in Diyala.

>> NAVAI: I hear of a place near to Muqdadiya where kidnappers have supposedly disposed of their victims.

So our guide says we can't stop, we can't get out of the car, because there are militias all around us and they're constantly patrolling.

It's too dangerous to get out.

We've just stopped.

They say it's safe for us to check this bit out.

We'll be hidden by the grass that's growing on the side.

Off camera, local people tell me the bodies are often thrown over this bridge.

This is cellphone footage, given to us by a fisherman.

He says he discovered this body three months ago.

I track down the dead man's uncle, who's living in hiding.

He asks us not to reveal the family's name, as he says it would put them all in danger.

Witnesses told him what happened.

>> NAVAI: He tells me kidnappers are holding another of his relatives.

He doesn't know which militia group they belong to.

The family have decided not to pay a ransom.

>> NAVAI: I ask a senior police official in Diyala about the allegations.

He's a Shia who says he's appalled by what's happening to his Sunni neighbors.

He says the federal police don't stop the militias because their ranks are full of active Badr members who won't go after their fellow fighters.

>> NAVAI: So what have you seen as a policeman in Diyala?

>> NAVAI: So you're saying the police are involved in kidnapping and killing in Diyala?

>> NAVAI: We've got to leave because it's coming up to sunset and the area's not even safe for locals here.

As I leave Diyala my guides show me abandoned buildings and untended farms.

Our guide is pointing out farms on the left-hand side here.

He's saying they were run by Sunni families and they've all fled.

They're completely abandoned now.

A number of residents give me cellphone footage they claim shows Shia militias burning Sunni farms.

And I hear many similar stories about farms being burned or bulldozed.

I try again to speak to the prime minister and other government officials about the many allegations in Diyala.

They won't talk.

But a senior adviser to the government, Ihsan al-Shimari, agrees to go on camera.

Why hasn't the government been able to do anything about the sectarian violence and these Shia armed groups?

>> NAVAI: Over the past two years, thousands of Sunnis have fled their homes in Diyala.

On the northern border of the province, I find a makeshift refugee camp, full of families.

Two years after their province was liberated from ISIS, they say they're too frightened to return home.

Sheikh Suliman Aliawi and his wife, Amal, tell me they've been warned never to return to their home village of Sinsil.

They say that in January 2015, a Shia militia-- they don't know which one-- gathered all men under 70 for security vetting, including five of their sons.

Amal went to the house where they'd been taken.

(man screaming) >> NAVAI: This is cellphone footage of what she saw.

Their five sons had been killed, as well as over 50 other men.

>> NAVAI: Mubarak's father.

>> NAVAI: They say their sons had nothing to do with ISIS.

>> NAVAI: The government announced an inquiry into what happened, but more than two years on, no findings have been released.

The Badr militia denies it was involved, but says the men were all ISIS members.

It's really striking that while the West is fighting the war against ISIS, most people we've spoken to here have told us they're much more scared of the militias.

I want to speak to someone senior in the Badr Organization.

So I travel to the northern city of Erbil.

Haitham al Mayahi is the political adviser to the head of Badr.

He says they don't condone abuse of Sunnis, but harsh treatment of ISIS suspects is justified.

>> To kill an ISIS member or to torture an ISIS member, this is abuse to you?

To me it's not.

This is the right way because he's a murderer, he has to be tortured and killed.

We are a country who are facing car bombing every day, suicidal every day.

If this happens to you, would you wait for a trial?

>> NAVAI: I've spoken to a Badr Organization member who told me he knows colleagues of his who kidnap and kill.

>> If you are very sure about that, that there are people who are kidnapping and killing and they are related to Badr, I assure you we can go together now, we'll take those people to justice, because I am very sure we not allow any mistakes in Badr.

>> NAVAI: I have even spoken to a Shia member of the federal police in Diyala, and he says that Badr Organization members have infiltrated the federal police in Diyala and he says that many times he has seen Badr Organization members kidnap in front of his eyes, he's witnessed it, he's seen men bound and gagged in the back of cars.

>> I'm not quite sure what you're talking about, because, um, I visit Diyala many times, and when we are there, people actually welcome us with warm feeling.

>> NAVAI: While I'm in Erbil, I hear of more allegations, not about Badr but once again about the Hezbollah Brigades, also known as Kata'ib Hezbollah.

We're going to meet a Sunni MP from Anbar who's been investigating the case of hundreds of Sunni men who have disappeared at a checkpoint manned by Kata'ib Hezbollah.

Now, he's one of only a few people who's been speaking out openly against the militias, and for that he's been receiving regular death threats.

Mr. Salmani.

Ahmed Salmani is one of Iraq's best-known Sunni politicians.

He monitors videos that militiamen share on social media.

He says this video shows Hezbollah Brigades militiamen at the Razaza checkpoint in Anbar province.

>> NAVAI: Oh, God!

It shows a man in militia uniform cutting off the ear of a prisoner.

>> NAVAI: That was horrific.

That was Razaza checkpoint?

This is where the men are going missing?

>> NAVAI: Relatives have given Ahmad Salmani the names of over 2,000 men they say disappeared from Razaza checkpoint.

He says militia insiders have told him the abducted men are in a network of prisons run by the Hezbollah Brigades around the town of Jurf al Sakhar.

>> NAVAI: Does the government know this is happening?

>> NAVAI: The defense minister has since left his position.

He doesn't reply to my request to talk to him.

I ask Vice President Allawi about the militia prisons.

Does the government know about the secret prisons run by the Shia militias?

>> Definitely.

But they don't want to confront these secret prisons because they are held and controlled by strong militias.

>> NAVAI: Like Jurf Al Sakhar prison?

>> For example.

>> NAVAI: Over 2,000 men and boys who were taken at Razaza checkpoint?

>> Yes, yes, yes, yes, yes.

So nobody knows why they are remaining in prison.

The issue here which really is frightening, there is no attention being paid by the government to tackle this, this problem of the arrests, intimidation, and tortures of the, of people.

>> NAVAI: The government has not said anything publicly about the disappearances from Razaza checkpoint or the prisons.

But according to human rights groups, only 65 of the men have been seen again.

They were held at a prison run by the Hezbollah Brigades in Jurf al Sakhar.

One of the men released from Jurf al Sakhar has finally agreed to talk to us, but only on condition of anonymity.

When he was released, the militia's parting words to him were that if he spoke about his experience, they'd hunt him down and kill him.

>> NAVAI: Instead of execution, he says the torture started.

>> NAVAI: I meet another man, who says he was held in the same prison.

He tells me the Shia militias are creating a new generation of enemies.

Are you worried that Sunnis may turn to violence to fight back?

>> NAVAI: Vice President Allawi agrees that militia abuses could drive Sunnis closer to ISIS, or Daesh, as it's called in Arabic.

We're hearing that the Sunnis now are talking of a new insurgency.

Does this trouble you?

>> It's possible, it's possible, it's possible we will see even a worse Daesh in the future.

More serious replacements will appear, and more dangerous, more cunning and more destructive, and this would not only limit itself to this part of the world.

It will travel and spill over into the whole globe.

>> NAVAI: The role of the Shia militias has become a major concern in the ongoing battle for Mosul, a mainly Sunni city.

The U.S. has urged the Iraqi government to keep the Shia militias out of the city, fearing sectarian violence.

For now, militia leaders say their forces will remain in the nearby countryside.

I'm heading towards Mosul to find out more.

(explosion) Are you filming?

So we're just on the road to Mosul and everyone's being stopped here, and you heard that big bang.

We think it's an I.E.D.

that's just been exploded.

There was a guy with a knife digging in.

We think he was trying to clear another one.

We're two miles from the frontline.

This neighborhood is not safe.

The next day, at this very location, three ISIS suicide bombers killed and injured dozens of civilians.

A Badr militia unit has agreed to meet us not far from Mosul.

They've been given the job of taking ISIS-held towns and countryside west of the city.

It's 7:00 a.m.

The unit is about to advance to a town which the militia has just recaptured.

Commander Saady Kadoom is watching the morning news, which is about ISIS atrocities.

>> NAVAI: Although many Badr units have been accused of mistreating Sunnis, Commander Kadoom says he and his men are fighting ISIS, not Iraq's Sunni civilians.

>> NAVAI: The Iraqi Army is stretched thin around Mosul.

They're relying on the militias to secure some of the towns won back from ISIS.

This is a Sunni village.

Most of the residents are no longer here.

I'm told they've been rounded up for security screening.

The guys are now moving on from this town, and they're now going to the next town.

This is what they do every few days.

They advance and they take territory from ISIS.

And what they leave behind is lots of graffiti.

And now there's a Shia flag flying from the Sunni mosque here.

(Arabic song playing on radio) >> NAVAI: The guys are actually listening to ISIS radio.

They love to listen to it, because it gives them motivation.

It's what drives them.

>> NAVAI: The unit reaches the town of Tal Abtah.

ISIS have built tunnels under the streets here.

The militias are still clearing them.

Suddenly, we're told to stop filming.

>> NAVAI: Why do we have to put the camera down?

>> NAVAI: This neighborhood is controlled by the Hezbollah Brigades, the militia accused of the Razaza and Saqlawiya disappearances.

The men we're with are nervous.

What happens when you go in their territory?

>> NAVAI: Eventually, Commander Kadoom and his Badr fighters reach their destination.

(gun firing in distance) >> NAVAI: What was that shooting?

>> Here, it's good, but maybe go to there, it's not safe.

>> NAVAI: Kadoom and his men are securing Tal Abtah's hospital.

They've been given the names of Sunnis who might be ISIS collaborators.

>> This picture for cutting the hand off someone.

>> NAVAI: They're now taking me to an ISIS tunnel, and ISIS have built all this network of tunnels in this area.

And this is how they operated, and this is how they fought these guys.

They'd pop out of these tunnels.

God, it's big-- it's a sophisticated tunnel.

Towards the end of my trip, I meet fighters from another group.

The Sayed Shuhada Brigades are powerful, with a representative in parliament.

They're a breakaway group from the Hezbollah Brigades, and, like several other militias, their main patron is Iran.

Their leader is Abu Alaa Al Waeli.

Could you have fought this war against ISIS without Iran's help?

>> NAVAI: And what support has your group received directly from Iran?

>> NAVAI: He says his militia also has men in neighboring Syria fighting for President Assad, who is backed by Iran.

>> NAVAI: I was born in Iran and have reported on the Middle East for more than a decade.

I know how rare it is for militia leaders to openly acknowledge Iran's influence.

Later, I find some local Sunni residents who have fled the fighting.

They seem eager to praise the militias for driving out ISIS.

>> NAVAI: But when I speak off-camera to a militiaman in Persian, he tells me the militia have detained many Sunni men from the town and are holding them in nearby prisons.

>> NAVAI: He also says it's common to find Iranian fighters among militias like this.

He says there are four in his unit.

>> NAVAI: On the edge of Mosul, I come across a familiar scene.

(crying) >> NAVAI: Sunni men are being separated from their families.

>> NAVAI: Some of them have been taken aside as ISIS suspects and they're lined up against the wall or they're on the floor.

But we've just been told... We've stepped away because they haven't been checked for suicide vests or for weapons, and the whole atmosphere here is tense.

The defeat of ISIS in this neighborhood hasn't made life any easier for the people left behind.

>> NAVAI: There are gangs of kids like this, and you can see they're cold and they're really hungry.

The conditions here are bad-- it's freezing.

They're desperate.

On my journey through Iraq, I've seen ISIS losing ground.

But it's come at a cost.

Mistrust between Sunnis and Shias seems greater than ever.

The challenge for Iraq now will be preventing this from starting yet another war.

>> Go to pbs.org/frontline to learn more about Iraq's Shia militias and their role in the fight against ISIS.

>> This is what they do every few days, they advance and they take territory.

>> Read an interview with correspondent Ramita Navai about her reporting in Iraq.

Visit our Watch page, where you can stream more than 200 Frontline documentaries anytime for free.

Connect to the Frontline community on Facebook and Twitter or pbs.org/frontline.

>> NARRATOR: Next time on Frontline...

The North Korea the regime doesn't want seen.

>> If people stop believing in the regime, that means central control is breaking down.

>> NARRATOR: With undercover footage and exclusive interviews, Frontline uncovers a new generation risking their lives to smuggle information in and out.

>> Any kind of uprising will probably fail, and all your relatives will be sent to prison camps.

>> NARRATOR: Inside "The Secret State of North Korea."

>> For more on this and other Frontline programs, visit our website at pbs.org/frontline.

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