When Khaled Meshaal slipped quietly out of Damascus in January, Hamas ended a decade-long stay in the Syrian capital. After almost a year of equivocating, last week Hamas finally came out against Bashar al-Assad and in support of the Syrian opposition movement. “I salute the Syrian people who seek freedom, democracy, and reform,” Ismail Haniyeh, prime minister of the Hamas government in Gaza, told a large crowd at Cairo’s Al Azhar mosque after Friday prayers.Meshaal, who has led Hamas since Israel’s 2004 assassination of Abd al-Azziz Rantissi, first opened Hamas’ Damascus office in 2001. When the Hamas leadership was thrown out of Jordan in 1999 for trying to undermine the Jordan-Israel peace treaty, Meshaal was welcomed by the Assad regime, which, as the self-described beating heart of Arab nationalism, has always played a role in Palestinian politics, often through backing terrorist groups.Given their sectarian differences—Hamas is Sunni and the Assad regime is composed almost exclusively of Alawites, a heterodox Shia minority—the relationship was always a bit brittle. And yet both parties calculated it was still worth it. Hamas got money and weapons from Damascus and Tehran. And Syria got another proxy force with which to fight Israel, while keeping its own borders peaceful.Since the Syrian uprising began last March, Hamas was uneasy as the Assad regime slaughtered Sunnis by the hundreds, including its Muslim Brotherhood allies. Nonetheless, with only Qatar offering to replace Syria as Hamas’ host, the organization stayed relatively quiet, even after the Syrian Navy fired on a Palestinian refugee camp in the port city of Latakia in August, and the death toll throughout the country mounted by the thousands.So, why did it take Hamas so long to take a stand in support of their fellow Sunnis? Some are speculating that Hamas may have struck a deal with the new Islamist-dominated Egypt. In any case, Hamas’ defection from the Iranian-led bloc could be a game changer.Ever since King Abdullah warned in 2004 of a Shia crescent, spreading from Iran, through the Shia communities in Bahrain and Saudi Arabia, extending through Iraq and Syria, and reaching all the way to Hezbollah on the eastern Mediterranean, the Sunnis have feared Iran’s rise to regional dominance. Perhaps the Shia, led by nuclear-armed Iran, would finally overturn almost 1,400 years of Middle Eastern history and depose the region’s Sunni majority. Or not.***You wouldn’t have known it from President Obama’s 2009 Cairo speech, but there is not—and since the death of the prophet of Islam, has never been—a unified “Muslim world.” Instead, there are countless divisions on every possible level—religious, political, class, even party splits, even within seemingly uniform groups like Hamas.Under the guidance of Ayatollah Ruhollah Khomeini, the Islamic Republic of Iran sought to bridge these differences by uniting disparate groups around the idea of Islamic resistance against a common enemy: the West and Israel. This earned Iran and its allies the affection of the Sunni Arab masses disheartened that their own rulers—in Egypt, Jordan, Saudi Arabia, and the Gulf’s other Arab states—had opted out of the war with Israel.But at this point, the Sunnis cannot help but see the Iranian project as an anti-Sunni movement. In addition to Assad’s murderous response to the Syrian uprising, Hezbollah, the Shia terrorist group, stands accused of the 2005 assassination of former Lebanese Prime Minister Rafik Hariri, a major Sunni figure. And from the perspective of Sunni powers like Saudi Arabia, Iran’s nuclear weapons program is less of an issue for Israel and the West than it is for them, since it will tilt the regional balance of power against the Sunnis.From the Sunni point of view, the Obama Administration has proven inept—or worse—at managing Sunni interests. The big concern for the Sunnis, especially the Saudis, is that the White House has yet to act decisively to stop the Iranians from getting a bomb. But there are other issues, too. Last week, the Saudi foreign minister stormed out of a “Friends of Syria” meeting that the Obama Administration helped organize in Tunisia to discuss how best to support the rebels. Conferences aren’t enough, said Saud al-Faisal, who explained that arming the opposition would be an “excellent idea.”The White House is loath to do so for fear that this might lead to a regional war—the same reason, say administration officials, that a military attack on Iran would be a bad idea. However, as the Hamas shift makes clear, there is already a regionwide war under way: Sunni vs. Shia.The real question is: How will Hamas’ defection from its Shia patrons—Syria and Iran—affect the region’s most pressing issue, Iran’s march toward nuclear weapons? Hamas’ move doesn’t exactly clear the way for an Israeli strike, but at the very least Iran will have to assume that a group putting Sunni interests over Iranian ones is no longer a reliable asset.In Syria, Assad is consumed with his own survival. Hezbollah is prepared to retaliate against Israel on behalf of its Iranian overlord. But Iran might think twice about giving the order. Tehran has spent many hundreds of millions of dollars on its Lebanese ally, but there is no guarantee that this expensive investment survives the next round with Israel. Why throw away Hezbollah if the damage is already done to the Iranian nuclear weapons program?In the past, the Israelis were concerned that they might drag American troops into the crossfire, but after the U.S. withdrawal from Iraq, there’s one less card for the Iranians to play. The Iranians could very well fire on Sunni targets across the Gulf, but that would only make more obvious the anti-Sunni nature of the Iranian regime and further inflame the regional majority against the Shia.***You can bet that the Obama Administration won’t see things this way. The White House can’t see the real war that’s already under way because it understands the Middle East through the lens of the Palestinian-Israeli conflict. This was President Obama’s conviction when he came to office, and no matter how much evidence Israel or Washington’s Sunni allies provided about Iran being the major strategic threat, he persisted in the belief that a peace deal between the Palestinians and Israelis was the core conflict. From the White House’s perspective, pressuring the Israelis to sign a deal with the Palestinians would make everything else fall into place.The only reason that the administration’s rough treatment of Israel has been relatively tempered of late—and even recently, Defense Secretary Leon Panetta demanded that Israel “get to the damn table” to negotiate with the Palestinians—is that the White House doesn’t want to risk Jewish support in an election year.Rather than seeing Hamas’ defection as a reflection of the Sunni-Shia conflict, the White House will read Hamas’ distancing from Iran as a sign of moderation—and it will work tirelessly to nurture Hamas as a peace partner. If Obama wins again in November, this will be a pillar of the White House’s Middle East policy.Lee Smith is the author of The Consequences of Syria.