After the 12-Day Israeli War on Iran: Iraq Caught Between Sistani’s Fatwa and Khamenei’s Shadow

In light of the 12-day Israeli war on Iran, Iraq’s Shiite religious authority renewed its call for arms to be limited to the state alone and warned against returning to what it described as “eras of oppression and tyranny”—a reference to the period before the 2003 U.S. invasion.

On June 13, 2025, the Israeli Occupation launched strikes that killed dozens of Iranian military commanders and nuclear scientists. Iran responded with missile strikes on Tel Aviv; Washington then targeted Iranian nuclear sites. A full ceasefire was declared 12 days after the war began.

Preserving Gains

In its first statement after the ceasefire was announced, Iraq’s top Shiite religious authority, led by Ali al-Sistani, renewed its call to limit arms to the state alone—a position it had already made in a similar appeal seven months earlier. That earlier call had failed to sway the armed factions, most of which remain loyal to Iran’s Supreme Leader under the principle of Wilayat al-Faqih (also known as the Guardianship of the Islamic Jurist).

While Sistani’s 2014 fatwa of “defensive jihad” provided the religious basis for forming the Popular Mobilization Forces (PMF)—Iraq’s largest paramilitary umbrella—his influence no longer extends over several groups that had existed even before the fatwa. Some of those factions formally follow the leadership of Iran’s Supreme Leader Ali Khamenei.

Abdul Mahdi al-Karbalai, Sistani’s representative in Karbala, said Iraq is not insulated from what he described as a “battle between justice and tyranny” unfolding in the region, warning that the current moment is exceptionally dangerous.

Speaking on June 26, al-Karbalai warned that Iraq cannot remain untouched by the region’s escalating turmoil, calling on Iraqis to stay alert and clear-eyed. He stressed the need to rebuild the country on strong and stable foundations.

Addressing government and political officials, he called on them to fear God, protect the country’s interests, and defend its hard-won gains, adding that Iraq must not return to past eras of oppression and injustice despite accumulated failures and shortcomings.

He emphasized the need to correct the current path, make up for lost ground, and prevent foreign interference in all its forms, while reiterating the demand to limit weapons to the state and fight corruption.

On November 4, 2024, during a meeting with the new UN representative in Baghdad, Omani diplomat Mohamed al-Hassan, Sistani had made similar demands—calling for the enforcement of rule of law, exclusive state control over weapons, and combating corruption at all levels. He also cautioned that the road ahead for Iraqis to achieve these goals remains long.

In line with this position, the U.S. has also pushed Baghdad to disband the armed factions. According to Ibrahim al-Sumaidaie, political advisor to Iraqi Prime Minister Mohammed Shia’ al-Sudani, the U.S. warned that if the government does not do it, it would be done by force. This was echoed by Parliament Speaker Mahmoud al-Mashhadani in a separate interview in December 2024, in which he said that President Donald Trump had personally urged al-Sudani to ensure weapons remain under state control.

On October 24, 2024, al-Sudani himself declared that only the state has the authority to declare war or peace, and anyone acting outside that authority would be confronting the state directly, which derives its power from the constitution and the law.

Since the U.S. invasion in 2003, Iran has backed the formation of multiple Iraqi armed factions, including Kataib Hezbollah, Asa’ib Ahl al-Haq, Harakat al-Nujaba, Kata’ib Sayyid al-Shuhada, and Kata’ib al-Imam Ali. Though these factions follow Khamenei’s leadership, none intervened during the recent Israeli war on Iran.

Their inaction is attributed to prior Israeli threats to strike Iraq—a move Washington reportedly blocked, according to Foreign Minister Fuad Hussein. On March 18, 2025, Hussein said the leaders of the armed factions pledged to the Iraqi Prime Minister that they would not engage in any action that could provoke a strong retaliation against Iraq.

Before U.S. intervention to prevent Israeli Occupation attacks on Iraqi factions, many of these groups had launched rocket and drone attacks into Israeli territory in solidarity with Gaza following the events of October 7, 2023.

‘Losing Power’

Iraqi political analyst Ali al-Masari said Karbalai’s remarks are a clear sign of growing concern within the Shiite religious establishment about the potential unraveling of Shiite-led governance in Iraq. He suggested the warning stems from lessons learned in Syria after the collapse of Bashar al-Assad’s regime—another key ally of Iran’s regional bloc.

In an interview with Al-Estiklal, al-Masari dismissed the possibility that the armed factions would heed Sistani’s appeal, noting that their loyalty lies squarely with Iran’s Supreme Leader Ali Khamenei, whom they regard as their sole religious authority and ultimate political and military commander, whose orders they are bound to obey.

“These factions are unlikely to respond to any measures or calls from the current Iraqi government, which lacks the strength to disarm them. In contrast, the United States has threatened to dismantle them by force, making it more likely that they would surrender their weapons under pressure or coercion,” he said.

“Karbalai’s remarks might be rooted in broader concerns about possible political change in Iraq following the Israel-Iran war, especially with the upcoming parliamentary elections [scheduled for November 11, 2025]. The expectation is that Iran’s influence in Iraq may decline significantly.”

This is not the first time Karbalai has issued such warnings. On November 22, 2019, during a Friday sermon in Karbala, he cautioned Iraq’s political class that “spilling blood could lead to the fall of the regime and the transfer of power to others”—a thinly veiled reference to Iraq’s Sunni population.

Delivering the sermon from within the sacred Imam Hussein shrine, Karbalai stressed that rulers and officials must not treat the people as prey or exploit their resources through the power of the state.

He defended peaceful protests as a modern and legitimate means for oppressed people to voice their grievances, and urged those in power to allow such demonstrations and respond to them in accordance with principles of justice and fairness.

“History shows us that many revolutions and uprisings have erupted because people faced deep injustice and saw no other way to achieve freedom and change,” he said.

In October 2019, Iraq witnessed the largest protest movement in its modern history. Lasting a full year, the uprising demanded the prosecution of the ruling Shiite parties that had governed the country since 2003.

However, the protests were met with brutal repression by Iraqi security forces and Iran-backed armed factions operating under a joint command center led by Qassem Soleimani, the former commander of Iran’s Quds Force. Nearly 800 protesters were killed, and around 35,000 others were injured.

‘The Final Phase’

Ibrahim al-Sumaidaie, advisor to Iraqi Prime Minister Mohammed Shia’ al-Sudani, sees the recent call by the Shiite religious leadership to concentrate weapons exclusively under state control as a clear sign that the process of disarmament is moving closer to resolution.

The disarmament and integration of armed factions into state institutions was already part of al-Sudani’s government program. It was also one of the key conditions set by the ruling Coordination Framework for ending foreign combat presence in Iraq, he told Rudaw on June 28, 2025.

“The government had engaged in tough negotiations with the United States to end its combat deployment while retaining a purely advisory role; talks with the international coalition also aimed to shift military cooperation toward bilateral partnerships with key friendly countries,” he added.

As part of this effort, the government quietly held sensitive, high-level talks with armed factions, supported by a unified political stance and the backing of the religious authority. However, these efforts were delayed following the October 7, 2023 Operation al-Aqsa Flood and Hezbollah’s entry into the war.

Despite these setbacks, al-Sumaidaie stressed that the government maintained dialogue and worked to limit armed factions' activity to a minimum. At the same time, it launched operations to track down and restrict those responsible for launching drones.

He pointed out that this firm yet flexible strategy succeeded in keeping Iraqi factions from intervening in Syria during the collapse of Bashar al-Assad’s regime on December 8, 2024. As a result, the Iraqi government independently managed relations with Syria and its new leadership—effectively ending the armed factions’ role there.

“This final phase dialogue resulted in an agreement to keep the factions from intervening in the Israel–U.S. war, thanks to in-depth negotiations and their commitment to national interests by steering Iraq away from war.”

Al-Sumaidaie also noted that the prime minister, when asked about the situation, consistently emphasized the armed factions’ growing commitment to ongoing talks with the government. This, he said, is aimed at a gradual and flexible political dismantling of the weapons crisis within the state.

Iraqi political analyst Nizar Haidar said that the religious authority’s message is a warning to avoid letting the conflict spill into Iraq. The representative, he said, was urging Iraqis not to be dragged into the crisis or fall for its illusions.

Throughout the Israeli war on Iran, Iraq’s airspace was used as a corridor for drones and long-range missiles—highlighting the country’s lack of air defenses. This vulnerability has made it possible for external powers to exploit Iraqi skies for regional or internal score-settling.