The Muslim Brotherhood, the Islamic political organization that has been defanged in almost every area where it was once a key player, has driven a deep rift between the Gulf's two most powerful players.

Months of tension between Qatar and its neighbors came to a head last month when Saudi Arabia, Bahrain, and the United Arab Emirates (UAE) withdrew their ambassadors. Although the regional Gulf Cooperation Council (GCC) announced yesterday that the parties had resolved their disagreement, that will likely remain a surface-level fix unless Qatar abandons its support of the Muslim Brotherhood – something it has signaled it has no interest in doing.

The divisions over the Brotherhood between regional hegemon Saudi Arabia and its tiny neighbor Qatar center on the model of political Islam the Brotherhood represents, which combines the passion of religion with the power of the ballot box. Saudi Arabia, which sees this model as a threat to both its legitimacy and security, has branded the Brotherhood a terrorist organization.

Saudi Arabia is a formidable rival, but Qatar's new emir, who took over from his father last summer, is loath to mar his first year in power by kowtowing to Riyadh. Part of the reason is the importance placed in the Arab world on saving face.

But another reason for Qatar's intransigence is that it has banked on a form of governance fundamentally different from Saudi Arabia’s traditionalist model of monarchic rule. Qatar opted instead to back the system that upended the Arab world in 2011 – one that gives more power to the people.

“Having portrayed this as the right thing to do, then to turn 180 degrees … would undercut what they’ve been trying to build for the past 20 years,” says Gerd Nonneman, dean of Georgetown University's School of Foreign Service in Qatar.

He says Qatar has not only resisted joining Egypt and Saudi Arabia in labeling the Muslim Brotherhood a terrorist organization, but is also unlikely to close or hobble its satellite network Al Jazeera, widely seen as biased in the Brotherhood's favor; slip back into a follower's role with Saudi Arabia; or drop its pursuit of foreign policy independence, which Mr. Nonneman describes as “very much part of Qatar's bigger branding strategy.”

Feeling insecure

There are also domestic considerations. Qatar’s commitment to the Muslim Brotherhood abroad has acted as something of an insurance policy against religiously inspired political opposition at home, where the Brotherhood voluntarily disbanded in 1999.

While Qatar gave refuge to many Brotherhood members who were pushed out of Egypt and other countries, most notably the controversial and highly influential Egyptian sheikh Yusuf al-Qaradawi, those figures have steered clear of criticizing Qatar’s leadership.

In Qatar, "religion doesn’t play any role in articulating or forming oppositional sentiments, unlike in Saudi Arabia, Kuwait, Bahrain, or the UAE," says Mehran Kamrava, director of the Center for International and Regional Studies at Georgetown University's Qatar campus. "And the reason is that the state has patronized the Muslim Brotherhood, has presented itself domestically and regionally and internationally as the patron of the Muslim Brotherhood. And if the price of domestic tranquility in a very turbulent region is Saudi ire, it’s a small price to pay."

The Saudi leadership’s anger stems from not only its annoyance with Qatar's upstart ambitions, but also deep insecurity about its legitimacy. As the US gains greater energy independence through its own natural gas production and pursues a foreign-policy pivot toward Asia, Saudi leaders worry that Washington is not as committed to the energy-for-security alliance that has endured for decades.

In addition, Washington’s willingness to stand by when Saudi Arabia's 30-year Egyptian ally Hosni Mubarak was ousted – and to back the Brotherhood government that replaced it – made Saudi leaders worry that the US could support the Brotherhood on a regional level as well.

Saudi Arabia has long favored Islamist groups that eschew political involvement. Riyadh sees the Brotherhood, which has embraced politics, as an ideological rival and a model that threatens its own governance, since some of the strongest domestic opposition comes from Sunni Islamist groups.

“I think they see that there is a clash of legitimacy,” says Abdullah Baabood, director of the Gulf Studies program at Qatar University in Doha. “Therefore they see they are threatened not only internally but regionally, and they could be losing their ally [America].”

Other pressing concerns

Sensing a window of opportunity with Qatar’s relatively young and untested emir, Saudi Arabia has acted decisively to counter the revolution in Egypt.

It backed last July's military overthrow of the Qatar-supported Islamist government and gave an initial $5 billion in aid for the country’s ailing economy, as well as an additional $2 billion in January – far more than the $1.5 billion given each year by the US. It has pushed back on Qatar’s Al Jazeera network, and portrayed Doha as undermining the stability of the region through its support for Islamist rebels in Libya and Syria.

In announcing its withdrawal of its ambassador last month, Riyadh said that Doha had failed to uphold its commitment to the GCC not to support “anyone threatening the security and stability of the GCC whether as groups or individuals – via direct security work or through political influence, and not to support hostile media.” Yesterday’s deal involved an agreement on how to implement that previous understanding, according to a GCC statement.

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The deal could potentially pave the way for greater unity on common interests, including containing the violence in Syria and preventing Iran from obtaining nuclear weapons. Kuwaiti ruler Sheikh Sabah al-Ahmad al-Jaber al-Sabah alluded to the need for cooperation at an Arab League summit hosted by Kuwait last month.

“The dangers around us are enormous and we will not move towards joint Arab action without our unity and without casting aside our differences,” he said.