JUDY WOODRUFF: Now to the second of our three reports this week on the fight for Iraq.
Militia groups, made up mostly of Shia fighters, and many backed by Iran, have become instrumental in the battle to drive ISIS from Iraq. But their presence on the battlefield makes them a controversial force, one with which the United States has deadly familiarity.
Tonight, again in partnership with the Pulitzer Center on Crisis Reporting, special correspondent Jane Ferguson and producer Jon Gerberg report.
JANE FERGUSON: These young men are holding the line on a remote hilltop north of Tikrit. They fire at any movement across the oil fields on the horizon, where ISIS snipers are dug in. Conditions are rudimentary. Each fighter has little with him beyond his gun.
AHMED, Shia Militia Fighter (through translator): The end of ISIS is on my mind.
JANE FERGUSON: Ahmed is not part of the Iraqi army. He is a member of Iraq's Hashd al-Shaabi, also known as Popular Mobilization Unit.
They are predominantly Shia militias, and the radical Sunni group ISIS, or Da'esh, as they're called here, is their sworn enemy.
AHMED (through translator): My ambition is the end of Da'esh in Iraq. I came in response to the fatwa, the doctrine to defend my country, my sacred places. My wish in life is the end of Da'esh in Iraq.
JANE FERGUSON: Like thousands of other Shia Iraqis, Ahmed heard the call of Iraq's senior Shia leader, Ayatollah Ali Sistani, who in June 2014 issued a religious command, or fatwa, to take up arms and drive ISIS from Iraq.
Iraq's security forces had collapsed when ISIS rushed in from Syria and seized a third of the country, killing Shias, who they believe to be heretics. So, while the military was in chaos, tens of thousands of young Iraqi men flocked to the militias instead.
AHMED (through translator): The fatwa opened the door for us, so we volunteered with the Hashd militia. Ours is a belief and a will. We came because of our belief, not for a salary or anything else. We came because of our belief and our principles.
JANE FERGUSON: These troops have come from southern Iraq, and they're holding the front line in this whole area. The Iraqi army are nowhere to be seen, and they are camped down here, with ISIS positions just over the front line.
Many of these fighters, who have lived for months on the front lines now, were civilians with no military experience until they faced ISIS.
JUMAA AL-AYAME, Shia Militia Fighter (through translator): Even the army didn't take in volunteers in such numbers. We have huge numbers. We came like this, no training centers, nothing.
JANE FERGUSON: Their presence has been essential to the battle. ISIS has been pushed back from many areas, and the Hashd militias have played a major role in battles against the group.
But the actions of heavily armed Shia fighters in Sunni areas of Iraq have been deeply divisive. They're also accused of war crimes, such as beheadings, killings, and torture of Sunni residents in areas they have fought in. Human Rights Watch has called on the Iraqi government to rein them in, saying that, in vengeance for ISIS atrocities, they have attacked Sunni communities.
Belkis Wille is senior Iraq researcher for Human Rights Watch based in Kiev. We spoke with her via Skype.
BELKIS WILLE, Human Rights Watch: These are segments of the population that are being singled out for allegiance with ISIS, whether or not these individual members of the community are actually affiliated with ISIS. And the Popular Mobilization Forces has chosen to really single out this community and to carry out these revenge attacks on them outside of the military structure.
They have this ability to carry out these abuses, to carry out these revenge attacks with complete impunity.
JANE FERGUSON: When Fallujah city was retaken from ISIS in June, the Hashd al-Shaabi were accused of detaining over 1,000 men who fled the city. Some 600 are still reportedly missing.
This is a problem for the U.S.-led coalition. The Hashd al-Shaabi militias are fighting alongside U.S.-backed Iraqi army forces and benefiting from American airstrikes.
COL. JOHN DORRIAN, Coalition Spokesperson: Prime Minister Abadi has said that those alleged abuses definitely need to be investigated, and those responsible, if they did occur, need to be held to account.
So, we're going to work with the Iraqis on making sure that we set conditions to reduce as much as we can the possibility for human rights abuses. But it's a very complicated battlefield.
JANE FERGUSON: Shia militias like these are funded and supported by Iran and are a powerful tool of influence for the Iranian regime on their neighbor Iraq. There is plenty of bad blood between them and the U.S. military.
Some of these groups were responsible for killing American soldiers during the war here, seen by many as Iran's way of bleeding the U.S. effort, says Michael Eisenstadt. He served as both a civilian and an army officer in Iraq during the occupation. He is now at the Washington Institute.
MICHAEL EISENSTADT, The Washington Institute for Near East Policy: Many of them were involved in a low-level insurgency against the United States and have American — the blood of American soldiers on their hands. We don't want to operate in the same battle space as them. It creates a lot of problems.
JANE FERGUSON: Yet, as a major force fighting ISIS, they are technically on the same side as the U.S. in this war. However, their commander views America with deep suspicion.
JAFAR HASSAN, Shia Militia Fighter (through translator): Hashd al-Shaabi doesn't trust America. They're not here to fight ISIS. We are here to fight ISIS and fight them properly.
JANE FERGUSON: In fact, to him, the Americans have other intentions beyond ISIS or even Iraq.
JAFAR HASSAN (through translator): They want to control Arab countries and establish bases close to Iran. They have intentions against Iran, clearly.
JANE FERGUSON: But America's support of Iraq's security forces has effectively brought the U.S. into an indirect alliance with Iranian-backed groups. That is not by choice, says Eisenstadt.
MICHAEL EISENSTADT: But they also play a role in Iraq's efforts to emerge as the dominant outside power in Iraq and to kind of supplant the U.S. in this role. We don't have control over who participates in the fight on the ground, although we're putting a lot of pressure on the Iraqi military not to rely on these groups.
JANE FERGUSON: After this battle, the tens of thousands of young recruits to the Shia militias will have to find a new purpose.
AHMED, Shia Militia Fighter (through translator): When Da'esh ends in Iraq, I'm going to work. When this fatwa was first issued, I was sitting doing nothing. If I finish, I will go back to the way I was.
JANE FERGUSON: They are, however, unlikely to all return home. And the continued existence of armed militias beyond full government control could destabilize Iraq long after ISIS is gone.
For the PBS NewsHour, I'm Jane Ferguson in Tikrit, Iraq.