RENEE MONTAGNE, host:

This is MORNING EDITION from NPR News. I'm Renee Montagne.

In modern times, the two branches of Islam - Sunni and Shia - have co-existed peacefully, for the most part. That began to unravel in the latter part of the 20th century - challenged first by the Islamic revolution in Shiite Iran, then by the rise of both Sunni and Shiites fundamentalism, and now by the war in Iraq.

When the U.S. invaded Iraq, it didn't set out to deepen the divide in the Islamic world. But that may be one of the most important outcomes of the war.

NPR's Mike Shuster has the fourth part of our series "The Partisans of Ali: The History of Shia Faith and Politics."

MIKE SHUSTER: The United States invasion of Iraq began on March 20th, 2003.

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MIKE SHUSTER: NPR reporter Eric Westervelt was with the U.S. Army when it encountered resistance outside of Najaf.

ERIC WESTERVELT: (Unintelligible) firing on U.S. positions here in the outskirts of Najaf. Okay?

(Soundbite of explosion)

Unidentified Man #1: Ah, shit! Man!

Unidentified Man #2: Take out a tiger over there?

SHUSTER: American leaders told the nation and the world that the Iraqis would view the U.S. as liberators, not occupiers - that the war would be over quickly, and that Iraq would return to peace. Those rosy predictions did not take into account the violent and oftentimes tragic history of Iraq, especially the aspirations of Iraq's often-brutalized Shiite majority, says Augustus Norton, professor of Middle East history at Boston University.

Professor AUGUSTUS NORTON (Middle East History, Boston University): When proponents of the 2003 Iraq war would argue that the Shia Muslims of Iraq were predominantly secular in orientation, they either ignorantly or conveniently forgot about this recent history, which has had the effect of pushing the Iraqi Shias away from secularism towards, if you will, higher levels of religious identification and religiosity.

SHUSTER: So, it should not have been surprising that Iraqi Shiite clerics and Shiite political parties immediately seized the initiative, pressing for quick elections and a representative government.

Yitzhak Nakash is author of "Reaching for Power: The Shia in the Modern Arab World."

Professor YITZHAK NAKASH (Author, "Reaching for Power: The Shi'a in the Modern Arab World"): For well over a century, Shiite clerics have led movements, advocating parliamentary rule and just governance in the Middle East. In post-Baath Iraq, clerics have again taken the lead in large part because there's hardly any form of secular civil society in the country today that can act as the nucleus of an Iraqi political system.

SHUSTER: Until the overthrow of Saddam Hussein, the Shia never governed a modern Arab state. They were in control in Persian Iran, but the Sunnis led most Arab states in the Middle East. The change in Iraq was a shock, says Juan Cole, professor of Middle East history at the University of Michigan.

Professor JUAN COLE (Middle East History, University of Michigan): The Shiites have an Arab Shiite champion. And this is a new thing, that Baghdad has emerged as a center of Arab Shiite power.

SHUSTER: That provoked a violent backlash among Sunni Arabs in Iraq.

Unidentified Man #1: (Foreign language spoken)

Unidentified Man #2: He's saying that the (unintelligible)…

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SHUSTER: A car bomb explodes at the Shiite Shrine at the Imam Ali in Najaf in 2003, as NPR's Ivan Watson conducted an interview there. The Sunni insurgency first targeted American troops, but soon - with the involvement of al-Qaida in Iraq - attacked the Shiites as well. The targets: Shiite holy sites, Shiite neighborhoods in Baghdad and elsewhere, and ordinary Shiite civilians, thousands of whom have been abducted and murdered.

And then a year ago, came the bombing of the Askariya Shrine, a mosque directly connected to the story of the Twelfth Shiite Imam, the messianic hidden Imam. In 2006, the Shia fought back through militia attacks and murder. Shiite-Sunni violence now predominates in Iraq, notes Wayne White, a former senior intelligence officer for the state department.

Mr. WAYNE WHITE (Former Senior Intelligence Officer, U.S. State Department): It went virtually off the scale with the attack on the mosque. And essentially, a cycle of violence has been generated, initiated by al-Qaida in Iraq, which deliberately attacked Shia targets with suicide bombings in the expressed hope of provoking just this sort of confrontation. And they succeeded all too well.

SHUSTER: The U.S. claimed that Iran was responsible for much of the violence in Iraq. There's no question that the Shiite government in Baghdad has a close relationship with Tehran. But that's far from the whole story, says Vali Nasr, author of "The Shia Revival."

Dr. VALI NASR (Author, "The Shia Revival"): It is not Iran that is right now a threat to the political power, to the livelihood, to the sense of security of Iraqi Shias. It's the war with their Sunni countrymen that is the main threat.

SHUSTER: At the same time, top Shiite clerics in Iraq worked hard to pursue their own model of government, distinct from the Iranian rule of the mullahs. Iraq's senior cleric, Grand Ayatollah Ali al-Sistani - although born and raised in Iran - advocated a political future for Iraq that is far different from the Iran's, says Augustus Norton.

Professor NORTON: In my view, Ali Sistani does not see the Islamic republic model as implemented in Iran, as all appropriate for Iraq. And instead he understands the role of clerics like himself as being outside of the political system.

SHUSTER: Ayatollah Khomeini of Iran created the model of the Islamic republic, with all power resting in the hands of the clerics. Although this has been the government of Iran for more than a quarter century, there are doubters - in Iran as well as in Iraq and throughout the Shiite world, says Vali Nasr.

Mr. NASR: The popularity that Ayatollah Sistani has in many places in the Shia world, including in Iran, really underscores the fact that Khomeini's theory is still facing theological difficulties within Shiism, because Iran's against the grain of the entire Shia religious development.

SHUSTER: Still, not all of Iraq's Shia agreement.

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SHUSTER: Street fighting in Najaf in 2004. Twice that year, the Shiite militia known as the Mahdi Army attacked American troops. Ayatollah Sistani mediated an end to that fighting but since this militia has spawned neighborhood defense forces as well as anti-Sunni death squads. It catapulted its leader, the young firebrand cleric, Moqtada al-Sadr, into a prominent role in the Iraqi government.

Some in the U.S. claimed he or other Shiite figures are surrogates for Iran. But Wayne White(ph) doesn't see it that way.

Mr. WHITE: I think Iran is a secondary actor right now in Iraq, along with Syria and Saudi Arabia, that the internal dynamic, the viciousness of the fighting on the ground, is very much being stoked up by communal problems inside of Iraq itself.

(Soundbite of chanting)

SHUSTER: The call to prayer in the grand mosque in Mecca. The escalating sectarian violence in Iraq has become a great concern of the Saudi monarchy, fearful that it may spread to the kingdom's own Shiite minority, which lives near some of the most valuable oil fields in eastern Saudi Arabia.

The Saudis and other Sunni leaders became even more uneasy when war broke out last summer between Israel and Hezbollah, the Shiite militia in Lebanon.

Mr. NASR: For the firs time, Arabs break rank in the middle of a fight against Israel.

SHUSTER: The Sunnis did not automatically support Hezbollah's actions against Israel, says Vali Nasr, because they feared it represented the strengthening of Shiite power and Iranian influence.

Mr. NASR: A group of Sunni Arabs, Jihadis as well as kings and presidents, adopt a sectarian posture towards Hezbollah.

SHUSTER: In response to the chaos, the United States found itself siding overtly with Sunni leaders and nations. Yitzhak Nakash says that does not take into account the full record of Shiite politics in recent years.

Mr. NAKASH: The increase in acts of violence by Shiites against Western targets since the mid-1990s has stood in contrast to the growth of Sunni-sponsored terrorism by al-Qaida and other militant groups. A strategy that all Shiite groups have condemned, including the Lebanese Hezbollah organization, the Sadr movement in Iraq, and the hard-line regime in Iran.

SHUSTER: History does not seem to be the preferred guide as the U.S. makes its way of the chaotic upheavals of the Middle East today.

Mike Shuster, NPR News.

MONTAGNE: Tomorrow American faces the rising power of the partisans of Ali. And you'll find a slide show narrated by Mike at NPR.org.

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MONTAGNE: This is MORNING EDITION from NPR News.

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