After the fall of Mosul in July, Grand Ayatollah Ali Sistani issued a religious edict (fatwa) calling on Iraqi “citizens to defend the country, its people, the honor of its citizens, and its sacred places”. That is, to come defend their religion in a holy war against ISIS.

Sheikh Raad says that in the initial days after Sistani’s fatwa, men as old as 60 came to his small offices begging to fight to hold back ISIS and Sunni-led insurgents.

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According to Iraqi Deputy National Security Adviser, Dr Safa Hussein al-Sheikh, the Kata’ib Hezbollah militia, founded in the months leading up to the 2003 American invasion, is known for being smaller and more organised than the other Shia militias – and is considered highly secretive and adept, even by Iraqi intelligence standards.

“In the past, they had focused more on American targets – sophisticated, lethal, organised attacks that were not penetrated by the American or Iraqi intelligence,” Al Sheikh says.

When I visit, the 58-year-old Sheikh Raad sits wearily in his office wearing battle fatigues and several jewelled garnet and turquoise rings. With him is his young fourth wife, who surprisingly has her dark hair uncovered, and is heavily made up, dressed in tight trousers and high heels. She wants to film his conversation on her cell phone.

The Sheikh sees no irony in the fact that his current financial backer, Iran, was his former mortal enemy.

“Saddam imposed that war (the Iran-Iraq war) on the Shia people in Iraq and Iran,” he says. “It was Saddam’s fault. Not the fault of Iran.”

He says Kata’ib Hezbollah has about 4,000 fighters (Iraqi intelligence puts the figure closer to 1,000) that are “experienced from fighting in Amerli, Samara, but also have past experience fighting with Hezbollah in Syria”.

He himself goes back and forth to Syria, largely to protect Shia shrines near Damascus.  Much of it is done around the town of Sayyidah Zaynab – “Lady Zaynab” – a southern Damascus suburb that has a Shia shrine of the same name.

11_28_IranIraq_01Sadr City residents carry weapons as part of a local auxiliary militia to defend Baghdad, June 14, 2014. 

Some of his men, he says, were paid up to $700 (£446) a day by Iran to fight in Syria, but in Iraq they are getting far less, although he says Iran is arming his men with weapons – AK-47s, 12.7 mm heavy machine-gun and PKCs, a lighter, 7.62 mm, machine-gun used in many of the ­former-Soviet Bloc and Middle Eastern countries.

“Here, we are fighting for justice – for our faith – not for money,” he insists. “And don’t forget there is a big difference between Hezbollah in Iran and Hezbollah in Iraq. Philosophically, we have the same enemy – Daish (ISIS) and Israel – but we are fighting here for justice.”

To understand the presence of Shia militias in Iraq today, and the increasing sway of Iran, you have to go back to the legacy of the mass graves.

Shortly after Saddam Hussein, a Sunni who had systematically repressed the majority Shiites for decades by cracking down on their political parties and crushing Shia movements, fell from power in April, 2003, human rights workers and US investigators began exhuming graves where thousands of Shiites and ethnic Kurds had suddenly disappeared.

It is unclear how many Shias died during the Saddam years, but the figures range from 400,000 – 700,000 people. One grave near Baghdad alone held nearly 15,000 bodies. In another, near the southern city of Samawah, more than 72 were discovered, mainly women and children.

It is believed that up to 60,000 Shias disappeared from Baghdad during those years of terror, and ended up in pits of earth. Years later, when Saddam was finally gone, relatives would stand at the open graves, desperately tried to find something that could link them to their lost.

“I just wish I could feel him, touch him, see him,” said the sobbing mother of one of “the disappeared,” Hilu Issa, who went missing in 1980 at the age of 25. (I spoke to her in May 2003 just after the US-led invasion.)

The image of her vanished son remained ­frozen in time. “I need to know what happened to him.”

11_28_IranIraq_03Iraqi men line up for physical examinations at the main army recruiting center to volunteer for military service in Baghdad, Iraq, July 9, 2014, after authorities urged Iraqis to help battle insurgents. 

Saddam’s men typically came at night, and took people away without warning. Hilu’s mother never saw him again.

The day after Saddam fell, with the city of Bagdad in chaos, it was finally possible to put together pieces of the puzzle. In al-Haakimiya, a notorious Mukhabarat (secret police) prison used during his reign, I and an Iraqi colleague found ­evidence of brutal torture: restraints; blindfolds; torture instruments with hardened blood still on them; cells the size of bathtubs where desperate men had scrawled messages to the families they would never see again.

In post-war Iraq, the political tables flipped. After the American invasion, it was the Shias in power, the Sunnis who were being hunted.

When Haider al Abadi, a moderate Shia was designated prime minister last August, it was with the promise that his government would be more inclusive, and break the cycle of revenge and vengeance between Iraqi Shias and Sunnis.

But it is still hard to find any Shia family that has not, in some way, been touched by Saddam’s brutality and that does not still bear, in some way, a grudge or at least a quest for justice.

Last January, Nouri al Maliki, the former prime minister, and a Shia dissident under Saddam who held strong nationalistic ideals, launched a bombing campaign in Anbar Province, which is largely Sunni, apparently with the intention of driving out jihadists, aka, ISIS.

But human rights groups were concerned that the bombs were not just landing on the insurgents – but on civilian targets and neighbourhoods, in particular hospitals and residential areas. They saw the Anbar campaign as another widening of the endless sectarian conflict. As the bombing went on, it also became apparent that the Iraqi Security Forces (ISF) were simply not up to handling the job of pushing back ISIS. This opened the door to the Shia militias.

“What happened then is that some smaller Shia groups proposed they would join the fight,” says al-Sheikh, the deputy national security adviser, at his office in Baghdad.

“That was their first operation. There were initially probably only a couple of hundred Shia militiamen fighting then, until the fall of Mosul. Then it went in a different direction.”

When Mosul fell on June 10 2014, a wave of terror rippled through Baghdad’s population. Rumours and truths flew through the crowded markets and streets: ISIS fighters were a mere 20km (12 miles) from the city; ISIS were killing Shia and raping Shia women; ISIS had come to destroy all Shia Muslims.

Then came what the Baghdad morgue director called a “spike” in the number of Sunni disappearances and murders in the capital: clear reprisals for the ISIS killings. One June morning, he showed me and other reporters photographs of the work of the Shia militias: Sunni men ­tortured, beaten, murdered, their bodies thrown into fields, bloated and purple.

“It’s starting again,” he said, referring to the bloodiest period of the civil war, in 2006.

11_28_IranIraq_05Iraqi security forces and Shi'ite militias advance towards town of Amerli from their position in the Ajana, Sept. 1, 2014. 

He also meant that the Shia militias were back in control, filling in the military vacuum the ISF had left. Now the Shias were back– but this time as protectors of the people, with the government heavily relying on them.

“They call themselves jihadists, not militias,” says al-Sheikh. “They learned their skills from fighting American occupiers before they left.” (The Shia militias are believed to be responsible for a large proportion of the American combat deaths during the occupation).

It also brings another element to Iraq – the increasing reliance and influence of Iran, the Shia regional giant. Ever since the Iranian revolution in 1979, governments inside and outside the Arab world have feared Shia fundamentalism. But today in Baghdad, the men who rose up to fight against ISIS in the wake of them overrunning Mosul are overwhelmingly Shia. And they clearly have a religious as well as a military agenda.

Their money comes largely from Tehran, as do their weapons and best trainers, according to various sources in the Iraqi government and ­foreign analysts. The memory of a bitter war fought between Iraq and Iran from 1980-1988 in which nearly a million men died seems very far off in their memory.

Part of this resurgence of the Shia militias is the Grand Ayatollah Ali Sistani’s potent call to arms in July, following Mosul’s defeat.

The rush of Shia men of all ages – some even in their 60s who had fought in the Iran-Iraq – was staggering. They crowded to three or four central recruitment centers in Baghdad, were ­vetted, and about half of them were immediately dispatched to the belt of Baghdad. They then fanned out to ISIS fight alongside what was left of the demoralised ISF.

Five months on, with the American led ­campaign to “degrade and ultimately destroy” ISIS, underway, the Shia militias are the backbone of the Iraqi military operation.

As well as their American experience, their training also comes from the recent battlefields of Syria. Many were sent to help protect the Shia shrines from the Syrian Sunni rebels.

Iraqis insist there is nothing to fear from Iran’s heady presence in Iraq. They also say, in many ways, their allegiance lies with Iran.

“Who arrived here to save us three days after Mosul fell?” asks Dr Mowaffak al-Rubaie, a Member of Parliament and a former National Security Adviser (and best known as the man who led Saddam to the gallows and requested the guards loosen his handcuffs).

“Not the Americans. They only sent abysmal air strikes three months later when their citizens [the journalists James Foley, and later Steven Sotloff and Peter “Abdul-Rahman” Kassig] were beheaded. The speed of the Iranian response to Baghdad and Erbil was the next day.”

The Iranians sent 88 Russian-made Sukkhoi ground attack jets within weeks. They also sent their best fighters to train and advise – members of the elite Republican Guard. They sent pilots, weapons, and uniforms.

They also sent their military mastermind, Qasem Soleimani, leader of the Quds Force, whom many military leaders regard as an excellent, and highly strategic commander.

While usually secretive, ­Soleimani allowed himself to be photographed last September on the battlefields of Amerli, clearly sending a message to the West that ­Tehran was very present.

“He is here often in Baghdad, and Northern Iraq,” said one of Iraq’s leading Shia politicians who asked to remain anonymous. “Of course the Iraqi government knows about this. He is smart. He is also a man who loves war. He knows he is good at it.”

Qasem Soleimani's name has become synonymous with the handful of victories attributed to Iraqi ground forces 

As to why Iraq would trust Iran with their bitter legacy and so many dead, al-Rubaie shrugs: “We are faced with an existential threat – ISIS. You use any means in this case. You use any means.”

Many Iraqis see the militias as crucial for their survival. Sajad Jiyad, a London-based analyst with the Iraqi Institute for Economic Reform (IIER), explains that: “The militias are very powerful – but post-June they became even more so because there was a vacuum. They have good resources and committed fighters,” Jiyad says. ”Most of the Shia communities that suffer from car bombs and suicide attacks are actually glad to have their protection.”

And the fact that they are backed by ­Tehran? “The US has to reconcile with Iran,” says al-Rubaie. “With or without a nuclear deal. A US-Iranian reconciliation will be a huge contribution to the stability of the region.”

One of the main militias, Asaib ah Al-Haq, or The League of the Righteous, has leaders who have been jailed on terrorism charges during the US occupation. Asaib is the group most loathed by Sunnis who see it as a threat to their security. There is also believed to be a large criminal backbone at the heart of the militia, which is sometimes, but not always true.

“When anything bad happens in Baghdad, Asaib get blamed,” says al-Rubaie, making the militiamen sound more like naughty schoolboys than hardened killers.

Another is the Badr Brigades, formed in the 1980s during the Iran-Iraq war. A third is Sheikh Raad’s Kata’ib Hezbollah. Added to this are many other splinter groups that have risen up in various Shia neighbourhoods in Baghdad.

With the militias, however comes Iran’s ­powerful political and religious influence. The question is, what will happen to Iran when ISIS is eventually destroyed? (which al-Rubaie reckons might be 3-5 years militarily, but 7-10 years ­ideologically.)

Will the Iranians be willing, after this kind of investment, to pack it all in and go home?

Probably not, says al-Rubaie, but he says it’s time the West softened its “allergic” stance on Iran.

So what will be the end game? The fear is a Lebanese civil-war scenario, with militias from various sectarian divisions running riot throughout the country. Or that the Shias, tasting power now, and with Iran’s strong backing, are unlikely to give the Sunnis a fair hand when ISIS is eventually destroyed.

For Western diplomats, the concern is how the Shias see the future.

“Do they envision an Iraq that is completely Shia – where they are running little fiefdoms?” asked one.

Whatever their role in the future, for the moment, the militias are not going anywhere. They are crucial to ending the war against ISIS. One Western security adviser in Baghdad says that the Shias are “essential” to bolstering the flagging Iraqi Army.

“The truth is,” says Safa Hussein al-Sheikh, the Deputy National Security Adviser, “They prove to be more effective fighters than the Security Forces in many situations. They have experience from fighting the Americans, and from recently fighting in Syria. “

He pauses, and does not seem happy about his conclusion. “Fighting the Americans made them really experienced, really strong fighters.”

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SHIA WAR CRIMES

In recent months, Shia militias have been abducting and killing Sunni civilian men in Baghdad and around the country. These militias, often armed and backed by the government of Iraq, continue to operate with varying degrees of cooperation from government forces. For these reasons, Amnesty International holds the government of Iraq largely responsible for the serious human rights abuses, including war crimes, that have been committed by these militias.

Reports by families of the victims have been corroborated by Ministry of Health workers, who told Amnesty International that in recent months they have received scores of bodies of unidentified men with gunshot wounds to the head and often with their hands bound together with metal or plastic handcuffs, rope or cloth.

Some of the victims were killed even after their families had paid hefty ransoms. Several families told Amnesty International how they had received the dreaded call from the kidnappers, had searched frantically for the ransom money and had managed to pay it, only  to discover that their loved one had still been killed and their money gone.

From Absolute Impunity – Militia Rule in Iraq – a report by published by Amnesty ­International published this week