The rapid escalation of tensions in the Gulf over the past week is a serious and deeply troubling moment in the history of the Gulf Cooperation Council (GCC). But make no mistake, the GCC will survive this most severe of crises and it will ride out the storm as it has done many times in the past.

Since its inception in 1981, the GCC has never been a perfectly functioning body. The six states that comprise it still struggle to coordinate on economic, security and infrastructure matters, and have on many occasions clashed over the demarcation of borders and allocation of joint resources. However, like all families despite its myriad of disagreements and problems, the GCC holds together.

Although there can be no doubt that the GCC as a bloc will suffer reputational damage from this particularly serious episode, the hope on all sides is that the problem can be resolved quickly. For Qatar especially, hemmed in by land border closures and restrictions over regional airspace, it will be necessary to reach a quick and amicable compromise.

Nevertheless, bringing Qatar back into the fold and away from its current policies is unlikely to change the dynamics within the GCC very much. As expected, Kuwait has sought to mediate the dispute, while Oman has stayed out entirely, leaving Manama, Riyadh and Abu Dhabi to form a united front against Qatar.

The Iran factor

One of the key issues underpinning the decision by Saudi Arabia the UAE and Bahrain to isolate Qatar centres on its perceived softness toward Iran, and comments attributed to the Emir that Doha maintained good relations with Tehran. Comments that the Qataris strenuously deny were ever made.

The GCC is primarily still a collective security organisation, and the challenge of the Islamic Republic of Iran is still the biggest threat to its interests. With regard to Iran, Qatar has gone off message. And Riyadh -currently in the midst of a regional power struggle against Iran in Yemen, Lebanon, Syria and Iraq – is particularly aggrieved that a Gulf ally would stray off course.

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But regardless of what media pundits and talking heads say over the coming days, the GCC is not unified in its policies toward Iran, and it has never been. Kuwait seeks a balance in its own relations with Tehran, as does Oman which frequently plots an independent path, while Dubai relies on Iranian trade for one third of its economic productivity. In fact, it is the Qataris who by and large struggle to reconcile their distrust of Iran with the need to formulate pragmatic policy toward it. To this extent, the Qatari view of Iran is far closer to Saudi than elsewhere in the Gulf.

More problems in the future will surely lie ahead, but alarmist analyses misunderstand that in the Gulf disagreements subside with time, no matter how severe.

Outside of the Gulf, the GCC has maintained a much more aggressive posture vis-a-vis Iran, most importantly of all fighting the Iranian-supported Houthis in Yemen. With the exception of Oman, which prefers a quietist approach, there is very little daylight between the other Gulf nations and the belief is that Iranian interference in the region must be resisted at all costs. Qatar does not sit outside the GCC consensus on this issue, and it is likely that in the coming months Qatar will restart its contribution to Saudi-led operations in Yemen, after having been removed from the coalition following this recent flare-up in tensions.

Political Islam

Another important reason for Qatar’s isolation centres on the perceived threat of political Islam to the Gulf monarchies. This is perhaps the biggest point of difference between Qatar and the UAE, and also explains why Egypt has decided to cut ties with Qatar.

Qatar’s policies post the 2011 revolutions in the Arab world saw it courting a whole host of actors, many of whom had Islamist connections. This is a particular bone of contention for the UAE and Egypt, who are deeply unhappy with Qatari behaviour. It is likely that on this file Doha will have to bend to the GCC’s collective will. Simply put, Abu Dhabi and Riyadh will not back down until Qatar divorces itself from its regional alliances.

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Important to note is the influence of powerful international actors in the West who guarantee the Gulf’s security. Although US President Donald Trump has waded into the diplomatic furore, clearly signalling his displeasure with Qatar, US assets in the country are too valuable to risk. The US, United Kingdom and France are highly unlikely to take sides in this dispute. Likewise, eastern energy consumers China and Japan are unlikely to jeopardise their own energy security by breaking off relations with the Qataris, and a swift return to business as usual is in the interest of all parties.

Although the current situation is severe, the GCC will not emerge a fundamentally altered structure, nor will its collective deterrence be enhanced. More likely to emerge is the same slightly dysfunctional GCC structure, just with a quieter Qatar, more likely to play by the rules and tamp down its regional ambitions. Given that Riyadh already leads the GCC on a number of files – for example in Yemen, Syria and Horn of Africa- this will actually make little structural difference to the Middle East’s regional politics, the region’s myriad problems and unstable nature remain.

The question for Saudi Arabia, in particular, is what to do about all these problems once this spat with Qatar is over, and how best to mobilise the GCC to deal with those problems. For all the goodwill Mr Trump has shown Riyadh, it is unclear how this favour is transformed into a genuine policy to roll back Iran from the region, as well as to stabilise five Arab countries that are havens for non-state actors, including the Islamic State of Iraq and the Levant (ISIL, also known as ISIS) and al-Qaeda. In order to turn their eye toward fixing these problems, the last thing the Saudis need is a lengthy argument with Qatar.

The GCC will come back together after the storm, bruised and battered but not broken. More problems surely lie ahead in the future, but alarmist analyses misunderstand that in the Gulf disagreements subside with time, no matter how severe.

Michael Stephens is a research fellow for Middle East studies and head of the Royal United Services Institute in Qatar.

The views expressed in this article are the author’s own and do not necessarily reflect Al Jazeera’s editorial policy.