Iraq and its security occupy a central part in the debate about a possible nuclear agreement between Iran and world powers. The Gulf Arab states fear that Tehran, boosted by the relaxation of economic sanctions, will try to expand and consolidate its “hegemonic” grip over the Middle East.

According to this argument, Iranian hegemony will above all affect Iraq, where Tehran seeks to install a government in thrall to it, hindering the formation of a viable democratic system in its western neighbour. The domestic and foreign exponents of this view point to the growing power of Tehran-backed Shia groups fighting the so-called Islamic State (Isis) as proof of attempts to plant an Iranian “deep state” in Iraq, allegedly similar to Hezbollah in Lebanon.

Such concerns are legitimate but exaggerated and even misplaced. Iranian influence is unlikely to produce a state within the Iraqi state, even if some elements in Iran desire it. And this holds regardless of whether the nuclear negotiations are successful or not.

Shia paramilitary forces are undoubtedly on the rise in Iraq, and this may intensify sectarian fault lines. David Petraeus, who commanded US troops in Iraq during 2007-2008, has voiced concerns over reports of sectarian atrocities committed by the Shia Popular Mobilization Units (al-Hashd al-Sha’bi or PMUs) as well as by Iraqi security forces.

Human Rights Watch has accused the PMUs of looting and destroying Sunni Arabs’ property. Although PMU commanders have invariably condemned these acts and promised to bring the perpetrators to justice, their recurrence is likely to exacerbate the chronic distrust between Sunni Arabs and the Shia groups that make up the security backbone of the central government in Baghdad.

More worrying for Petraeus and many Arab politicians in the region, however, is the increasing influence of Iranian Revolutionary Guards - especially its overseas arm, the Quds Force - on which the bulk of PMU forces rely for logistical support and advice.

“If Daesh [the Arabic acronym for Isis] is driven from Iraq and the consequence is that Iranian-backed militias emerge as the most powerful force in the country - eclipsing the Iraqi security forces, much as Hezbollah does in Lebanon - that would be a very harmful outcome for Iraqi stability and sovereignty, not to mention our own national interests in the region,” Petraeus warned in an interview with The Washington Post. John Brennan, director of the CIA, has made similar comments about Iran’s “very aggressive and active” role in Iraq.

But this is not the entire picture, and represents a skewed conception of the reality on the ground. There are significant factors in play that undermine prospects for the PMUs becoming a force operating on behalf of Tehran outside the jurisdiction of Baghdad. While most of Iraq’s Shia citizens might desire a prosperous and successful Iran next door, it would be an extraordinary stretch of imagination to claim they would favour turning their land into an Iranian satellite state.

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The latest outburst of Iraqi nationalism vis-à-vis Iran came in response to controversial comments on Iranian-Iraqi relations from Ali Younesi, advisor to President Hassan Rouhani on ethnic minorities and a former intelligence minister. “Currently”, Younesi said, “Iraq is not only part of our civilisational influence, but it is our identity, culture, centre and capital…Because Iran and Iraq’s geography and culture are inseparable, either we fight one another or we become one.”

Younesi’s comments drew stringent criticism from Rouhani’s rivals in the Iranian parliament where 109 deputies signed a letter demanding his dismissal. Younesi was reportedly summoned to the Special Court for the Clergy, where he was questioned about “statements against national security” before being released on bail.

But by suggesting an imperial belief in bringing Iraq into the orbit of Iranian civilization, Younesi set off a massive backlash in Iraq not only from Sunni Arab groups and personalities, but also from Shias. Grand Ayatollah Ali al-Sistani, the most revered Shia cleric in Iraq, was one who stepped forward in defence of Iraqi autonomy and sovereignty.

“We are proud of our country and our identity and our independence and sovereignty,” said Ahmad al-Saafi, Sistani’s representative, in apparent response to Younesi’s remarks. “While we welcome any help offered today from our brothers and friends in our fight against the terrorists and thank them for that, this doesn’t mean in any way that we would ignore our identity and independence.”

In their fight against Isis, Shia paramilitary forces derive their religious legitimacy primarily from Sistani as their chief “source of emulation” and from his fatwa, issued after the group’s takeover of Mosul in June 2014, calling on all able Iraqis to take up arms. Ever since, Sistani has consistently maintained that volunteers must operate under Iraqi state command.

By the same token, the PMUs are at the moment organised by a committee affiliated with the Iraqi National Security Advisory (NSA), which is accountable to the prime minister, Haidar al-Abadi. It is hard to believe that all PMU actions and moves are under the scrutiny of Baghdad, but the Iraqi government does maintain a degree of control, providing their salaries and fighting equipment according to the defence minister, Khaled al-Obaidi.

This goes some way to meet demands from Sunnis for the “institutionalisation” of PMUs as a means to bring them under state control. The former deputy prime minister and leading Sunni Arab Rafe al-Issawi, for example, said recently at the Brookings Institution in Washington that “some of the militias...[are] out of the total control of the central government...[and] without institutionalisation of paramilitary forces...there will be much more discontent”.

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Given the strength of nationalist sentiment across all Iraqi sects and the broad-based recognition of Sistani as a force for national unity, it will be difficult for Shia PMU groups to form a quasi-state in parallel to the Iraqi government once Isis is dislodged. In the eventuality of such a political outgrowth, the PMUs are bound to lose Sistani’s backing, and with it their legitimacy in the eyes of millions of Iraqi Shias who currently support them.

Moreover, PMU leaders and military commanders have so far shown little interest in taking that path. Hadi al-Ameri, the head of Badr Organisation, a long-standing Shia group with close ties to Iranian Revolutionary Guards, envisions a future for PMUs where the Iraqi state has the final say. “After Sayyed Sistani’s fatwa, we were left with no choice but to take up arms and fight,” he told al-Sumaria TV. “These are, however, the state’s arms. The Badr Organization doesn’t possess any weapons.”

In a similar vein, Qais al-Khazali, leader of Asaib Ahl al-Haq – another paramilitary Shia group with sympathies towards Iran – stressed during an interview with al-Ahd television that PMUs were “national factions for sure...part of the Iraqi state institutions, and committed to the decisions of the commander-in-chief [the Iraqi prime minister]”.

While seeing Iran as their major source of strategic depth, Iraqi Shias are reluctant to lose their majority position in the Iraqi state by creating a paramilitary force operating in parallel to the central government. Shia leaders understand these dynamics well, with a consensus emerging that a new National Guard will absorb the PMUs once Isis is done with and Ayatollah Sistani’s fatwa expires.

The National Guard is supposed to recruit locally and fall partly under the command of the elected local governments, mainly to assure the Sunni Arabs they will be included in running security. Both Shia and Sunni groups in Iraq are generally driven by a strong sense of nationalism and look forward to the rise of Iraq - given its strategic position, cultural heritage and natural resources - as a regional power on a par with Iran and Saudi Arabia. This is a promising cause that can soften and mature factional politics.

Hamdi Malik is a PhD student of sociology at Keele university, UK, and a frequent contributor to BBC Persian TV programmes. Maysam Behravesh is a PhD candidate in the department of political science at Lund university, Sweden, and editorial assistant of the academic journal Cooperation and Conflict