Back in 2004, President Bush went on NBC's Meet the Press to assure Americans that Iraq was not going to turn into an Islamist theocracy under the emerging Shia leadership.

"They're not going to develop that," said Bush, noting that he'd just met Abdul Aziz al-Hakim, the leader of the Supreme Council for the Islamic Revolution in Iraq (SCIRI). "I remember speaking to Mr. al-Hakim. I said, 'You know, I'm a Methodist. What are my chances of success in your country and your vision?' And he said, 'It's going to be a free society where you can worship freely.'"

Added the president: "This is a Shia fellow."

No matter that the president actually said "fella," inadvertently pronouncing the Arab word for "peasant." Even by then it was clear, and by now it is blindingly obvious, that not only is there no room for Methodists in Hakim's Iraq; there isn't much room for Sunni Arabs, either. Indeed, the central irony of the war in Iraq is that a military operation ostensibly designed to install a model democracy in Baghdad has created a regime dominated by benighted Shia Islamist theocrats and run by mullahs and activists allied with Iran.

Bush perhaps can be forgiven his naïveté about Hakim -- though the fact that the name of Hakim's organization includes the words "Islamic Revolution" might have tipped him off. Others, however -- including the hawks promoting the war in 2001–03 -- were fully informed about al-Hakim, SCIRI, and its origins in Iran. They knew that by toppling Saddam Hussein, they would unleash the Shia majority in Iraq. They knew that Al Dawa ("the Call"), the party of Prime Minister Nuri al-Maliki, had a long history as a terrorist-inclined Islamist secret society. They'd read the reams of intelligence dossiers -- compiled over decades by the U.S. intelligence community -- on SCIRI, Al Dawa, and their allies. And they had plenty of evidence that Ahmad Chalabi, the smooth-talking Shiite who brought SCIRI and Dawa into the inner circle of the Iraqi National Congress (INC), was a snake-oil salesman who made no secret of his own close ties to Tehran's ruling circles.

Today, virtually all of Iran's leading Shia political and religious leaders are either kowtowing to Tehran, beholden to Iran for support, or fearful of challenging Iran's dominant role. "Iran has leads into every single Shia group," says Ali Allawi, a longtime Shia opposition leader who served as Iraq's first postwar civilian minister of defense. "They have leads into ... SCIRI, into Dawa -- one of its wings is far more dependent on Iran than the other -- into [Muqtada] al-Sadr, and into politicians like Ahmad Chalabi."

All of which raises some obvious questions: How could the neoconservatives, bitter enemies of Iran's ayatollahs, have supported the rise to power of Iran's closest allies? Why, even after it became clear that their Iraq adventure had gone awry, did they continue to defend the Shia religious parties and Chalabi? And why, even today, does the White House use its "surge" to prop up Maliki's government, Hakim, and the SCIRI Islamists? Despite the government's pretensions to neutrality in the Sunni-Shia civil war, American forces are objectively backing one side in that war.

"Maliki's objective in the surge is for the Americans to kill as many Sunnis as possible, and do as little damage as possible to the Badr Corps and the Mahdi Army," says Bruce Riedel, a longtime CIA officer who ran Near East affairs at the National Security Council under President Bush until 2002, referring to the militias of SCIRI and Sadr. "And what you're seeing happening in Baghdad is exactly that: The Badr Corps and the Mahdi Army are staying off the streets, waiting for the surge to kill the Sunnis. What I don't know is whether [General David] Petraeus knows this as well. I can't tell."

To understand why the neoconservatives and many of their allies were so sanguine about the Shia rise to power in Iraq, it's necessary to grasp three fatally flawed assumptions that shaped their view.

First, the neocons and some Israeli strategists had long seen the Shia as "outsiders" opposed to the mainstream Arab (read: Sunni) nationalist current, and over decades had developed an affinity for the Shia as potential allies in the region, much as they saw the Lebanese Maronite Christians and other minorities in the Arab world.

"There existed a supercilious 'Shiaphilia' among certain academics, Iraqi political exiles, policy wonks and policymakers linked to the Bush administration," wrote Ahmed Hashim, author of Insurgency and Counter-insurgency in Iraq and a professor of strategic studies at the U.S. Naval War College. At the American Enterprise Institute and among partisans of Chalabi's INC, it was routine to speak of "de-Arabizing" Iraq after the fall of Saddam Hussein, a favorite theme of the INC's favored intellectual, Kanan Makiya.

Second, the neocons had been seduced by Chalabi, who convinced them that Iraq's Shia leaders would abandon their ties to Iran and rush to embrace a secular, pro-American political culture. Vali Nasr, author of The Shia Revival and a professor at the Naval Postgraduate School, attributes this to the neocons' "reading of the Israeli experience in the invasion of south Lebanon in 1982. That's why they had this vocabulary of 'They're going to greet us with flowers,' because that's what happened in south Lebanon -- the Israeli army was greeted by Shia villagers with flowers and rice."

Third, the neocons believed that moderate, nonpolitical Shia in Iraq would establish Najaf, the Iraqi shrine city that is the holiest place in Shia Islam, as a new center of gravity that would overpower Qom, the clerical powerhouse city in Iran. They believed that the "good Shia," supposedly "quietist" ayatollahs such as Ali al-Sistani, would emerge to present a frontal challenge to Iran's militant "bad Shia," followers of the Ayatollah Ruhollah Khomeini. A leading proponent of this theory was David Wurmser, a radical neocon who is currently Vice President Cheney's top Middle East adviser. "They deluded themselves into thinking that these links operated only one way -- with Najaf undermining Qom," says Nasr. "They assumed that it was Iraq that would influence Iran, not that Iran would influence Iraq."

On the eve of the U.S. invasion of Iraq, many astute observers of the Middle East were aghast at the prospect of American action haphazardly bringing Iran-linked political Shia fundamentalists to power. "In the prewar period we held a number of meetings and confrontations with prominent Arabs, and they were shocked at how American policy-makers were quite prepared to see a Shia-dominated Iraq," says Patrick Clawson, a neoconservative scholar and Middle East expert at the Washington Institute for Near East Policy. Israelis and moderate Arabs alike came to Washington to underline that message, says Clawson. "What I found repeatedly was they would make the rounds in Washington, and they would be in shock at just how much the U.S. government had thought about that, and decided that that was OK."

In March 2003, during the feverish run-up to the invasion of Iraq, it wasn't as if the U.S. intelligence community didn't have the goods on Iraq's Islamist exiles. "People who'd followed this issue for a while at the CIA and the State Department … knew that [SCIRI and its paramilitary arm, the Badr Organization] were extremely close to the Iranians and had spent more than 20 years either in Tehran or in Damascus, with very close relations to Iran, or in Europe, in places where they were closely affiliated with Iranian intelligence," says Riedel. "The SCIRI representative in London, Hamid Bayati, had very close relations with Iranian intelligence … The facts were well known within the national-security bureaucracy."

The story of SCIRI and Dawa is a tale of two families, the Hakims and the Sadrs, two of Iraq's most prominent religious dynasties. In some ways, especially today, the Hakims and the Sadrs are like the Hatfields and the McCoys: feuding clans that hold decades-old grudges. That partly explains the current enmity between Abdul-Aziz al-Hakim of SCIRI and the upstart cleric Muqtada al-Sadr and his Mahdi Army.

The Dawa Party was created in 1957–58, as the pro-British Iraqi monarchy crumbled to a coalition of Iraqi army officers and the Iraqi Communist Party (ICP). At the time, the ICP was the largest communist party in the Middle East, capable of bringing a million people into the streets, and the vast majority of its members were Iraqi Shia. Young Shia, then flooding Baghdad from the mostly Shia tribal countryside, were the backbone of the ICP; many joined the fledgling Baath Party, too. Desperate to stanch the Shia flow into the ICP and the Baath, the leading ayatollahs of Najaf's Hawza -- a "Vatican"-like Shia institution -- established the Dawa Party to mobilize Shia youth in opposition to communists, Baathists, and the nationalist left. Its chief founders were a pair of ayatollahs who were the granddaddies of today's Hakim and Sadr clans: Mohsen al-Hakim and Mohammed Baqr al-Sadr.

In 1960, the entire leadership of the political Shia Islamist movement for the next half century in Iraq got its start in the Dawa Party and a parallel institution called the Jamaat al-Ulama, both of whose original meetings took place in the homes of Sadr and Hakim. Sadr wrote the Dawa Party's founding principles, and Hakim's sons -- including Mohammed Baqr al-Hakim, the founder of SCIRI -- became two of Dawa's leading organizers. Both Mohammed Baqr al-Sadr (known as Sadr I) and Mohsen al-Hakim were anti-communist ideologues, and their Jamaat organization routinely issued pamphlets with titles like "Communism is the Enemy of the People." In 1960, Sadr I proclaimed a famous fatwa banning Iraqis from belonging to the ICP. That got the attention of Cold War U.S. diplomats in Baghdad, who held tête-à-têtes with Mohsen al-Hakim back then, according to Allawi.

Ironically, writes Faleh A. Jabar, in The Shi'ite Movement in Iraq, "[Dawa's] founding group sought to create a Leninist organization based on cells, chain of command, discipline, and obedience." Over the next two decades, Dawa would engage in a clandestine war against a series of Iraqi governments, including Saddam Hussein's. Its partisans frequently engaged in terrorist violence, and they were met with brutal repression in response. When the 1979 Iranian revolution drastically raised tensions between Iran and Iraq, where the Ayatollah Khomeini had spent 14 years in exile in Najaf, Saddam Hussein made Dawa Party membership a capital offense, and in 1980, he arrested and executed Sadr I. Many Shia were expelled or fled to Iran, where Khomeini was threatening to spread Iran's Islamic theocracy into Iraq.

The Sadr branch of Dawa, for the most part, stayed in Iraq, where it organized under the radar until 2003. The Hakim branch, on the other hand, fled to Iran, and an important rivalry began to develop between the two branches. Whereas the Sadrs took pride in their determination to resist Saddam Hussein inside Iraq, the Hakims hitched their wagon to Iran. SCIRI was founded in 1982, in Tehran, by the Ayatollah Khomeini and placed under the control of the Iranian intelligence service, SAVAMA, and Iran's Revolutionary Guard, with Mohammed Baqr al-Hakim and Abdel Aziz al-Hakim, sons of Mohsen al-Hakim, at its helm. Soon afterward, the Revolutionary Guard created the Badr Corps (which later changed its name to the Badr Organization), mobilizing thousands of Iraqi Shia from POW camps that swelled during the Iran-Iraq war.

"SCIRI's military and intelligence units were both actually managed by Iranians," according to Jabar. "With the creation of the Faylaq Badr [Badr Corps], intelligence and military affairs were taken from these units and conveyed to Badr. Despite SCIRI's talk of the Badr Army as an Iraqi organization, the force was under Iranian command. The commander of the force was an Iranian colonel." Specifically, Hakim's chief sponsor in Iran was the Ayatollah Ali Khamenei, then president of Iran, who in 1989 succeeded Khomeini as Iran's supreme leader, the position he still holds today.

Wayne White, who headed the State Department's intelligence unit on Iraq in 2003, had closely followed the rise of SCIRI and Badr in the 1980s. "Starting in 1982, we were getting a pretty good picture of the political part of it, and its leadership," says White, adding that the Iranians saw SCIRI as a potential pro-Iranian government-in-exile. For its first few years, explains White, Badr was poorly trained and disorganized, but by 1985 it had started to become a lot more professional. Perhaps 10,000 Iraqis made up the Badr force in the 1980s but the Iranians threw them into battle against their former country without regard for casualties. The Badr Corps "was badly decimated by the end of the war," says White.

In 1987, The New York Times reported that Khomeini "is believed to have a provisional Islamic revolutionary government under an exiled Iraqi Shiite Moslem clergyman, Ayatollah Baqr Hakim, waiting to be installed in Basra." A year later, at a Tehran soccer stadium, Baqr Hakim addressed a captive audience of Iraqi POWs, who chanted: "Under the leadership of Khomeini, we would like to fight!"

The evidence was incontrovertible: SCIRI and Badr were Iranian tools. Because the United States had tilted toward Iraq during the Iran-Iraq war, opponents of Saddam Hussein -- particularly Islamist ones tied to Iran -- were viewed unfavorably in Washington. That, however, began to change in the 1990s, in the aftermath of the U.S.–Iraq showdown over Kuwait.

From the end of the Gulf War, in 1991, until the invasion of Iraq, in 2003, both SCIRI and Dawa executed a deft pas de deux with the United States, conducting a dialogue that included off-the-record contacts, hallway meetings, and -- starting in 1998, with the passage of the neocon-inspired Iraq Liberation Act (ILA) -- official relations. The unofficial ties spanned the 1991 Shia uprising in southern Iraq, in which Iran and SCIRI played a minor, supporting role; the 1992 declaration by President George Bush Senior of a "no-fly zone" in Iraq's south, which brought the United States and Iraq's Shia closer together; and the creation of an organized Iraqi opposition.

There was a great deal of mutual suspicion, particularly since SCIRI and Dawa had both been linked to terrorism in the 1980s. In 1983, Dawa and the Hakims were widely reported to be behind the bombing of the U.S. Embassy in Kuwait, and Al Dawa was linked to a series of hijacking and kidnappings, often in alliance with Hezbollah, a Shia movement in Lebanon whose spiritual leader was closely tied to the Sadrs. In the mid-1980s, Dawa was placed on the State Department's list of terrorist organizations.

"In 1991, when we started talking to the Iraqi opposition -- and I was the senior State Department guy who dealt with them -- it was agreed not to talk to Dawa," says David Mack, vice president of the Middle East Institute. Quietly, however, U.S. contacts with SCIRI proliferated.

The vehicle for these was the Iraqi National Congress, established in 1991–92 by Chalabi, with the assistance of the CIA. Although SCIRI and Dawa had an on-again/off-again relationship with the INC, Chalabi worked tirelessly to broker contacts between Washington and the Tehran-based Islamist groups. In 1992, then–CIA Director Robert Gates delivered $30 million to the Iraqi opposition, while pressuring Saudi Arabia -- a Sunni kingdom that looked askance at the Shia Islamists -- to work with Hakim, according to reports at the time in The Washington Post and the Chicago Tribune. Soon afterward, Saudi Arabia sent hundreds of Iraqi POWs captured in the Gulf War to Iran so they could join the forces of SCIRI's Badr Corps. By 1996, the Clinton administration had regular contacts with SCIRI through Hamid Bayati, SCIRI's London representative.

In 1998, Chalabi, Richard Perle, and Paul Wolfowitz helped lobby the ILA through Congress, providing another stream of funds to the INC, and in 1999, SCIRI was officially designated as a qualified recipient of U.S. funds under the act. Mohammed Baqr al-Hakim made regular visits to Kuwait, where he consulted with U.S. diplomats and intelligence officers. According to Allawi, Frank Ricciardone -- the State Department official who served as liaison to the Iraqi opposition in the late '90s -- discreetly maintained lines of communications to SCIRI.

"The neoconservatives formed a small cell to win passage of the ILA, and money began flowing again to Chalabi," says Laith Kubba, the senior Middle East officer at the National Endowment for Democracy. "SCIRI was part of that set up. All of this was done through this broker, Chalabi. I do not tell you this lightly. I was there."

Kubba should know. For years, he was an Iraqi opposition insider, close to Dawa and the INC and a participant in all of the opposition's dealings with the United States. After the U.S.–led invasion of Iraq in 2003, he served as the official spokesman for Prime Minister Ibrahim Jafari. "And Chalabi was playing a double game," says Kubba.

Chalabi didn't hide his Iranian connection. He'd opened an office in Tehran -- ironically, with State Department funds. Early in 2003, I encountered Entifadh Qanbar, the INC's Washington representative and a top aide to Chalabi, at an American Enterprise Institute event. Who are you working with in Tehran? I asked. The reformers? The military? "No," he replied. "We are working with the hard-liners," including Khamenei.

There's no doubt that the AEI's hawks, and the Pentagon's, knew it, too. Says Bruce Riedel: "The hawks in the administration preferred to ignore this. When people like Chalabi said, 'I'm just using the Iranians,' they said, 'Great.' They took it at face value."

Despite myriad warnings about the danger posed by radical Shia Islamists in post-Saddam Iraq, the war planners moved forward. Ken Katzman, a Middle East specialist at the Congressional Research Service who worked with the U.S. intelligence community, says he personally warned policy-makers. "And I wasn't the only one," he says. "There was a lot of writing about how if you remove the Baath Party and the Sunni repressive apparatus, you're going to be left basically with the rise of Shia Islamists."

Warren Marik, a former CIA operative who was a liaison to Chalabi and the INC in the 1990s, is still amazed at the self-delusion that swept over administration officials. "I never talked to anyone [in the intelligence community] who had any illusion about who SCIRI and these guys were. They'd say, 'They're horrible. They'll turn against us.' But at the higher [policy] levels, people would say, 'Hakim, oh, he's a great guy. He's pro-American.'"

In December 2002, the Iraqi opposition met en masse in London with a team of U.S. officials, including Zalmay Khalilzad, the White House's liaison to Iraqi exiles. Thanks to a joint decision by the Iranian government and SCIRI, Hakim's people flooded the event.

"The [London] Congress was packed with an overwhelmingly Shiite representation; all Islamists were, one way or another, invited, endorsed, or at least not rejected by SCIRI, which had veto powers," wrote Jabar, in The Shi'ite Movement in Iraq.

According to David L. Phillips, author of Losing Iraq, who advised the State Department–led Future of Iraq Project in 2002 and who took part in the London meeting, the stunning SCIRI presence shocked U.S. officials and forced some of them, at least, to reevaluate the power alignment within the Iraqi opposition.

"When they discovered at the eleventh hour that Iran had much closer ties with these groups than we did, or ever would, the train had already left the station: The decision to go to war had already been made," says Phillips. "The realization came home in mid-December [2002], at the London opposition conference, when Zalmay Khalilzad was trying to compose an advisory group of Iraqis. [But] ... the key groups couldn't participate in a discussion with him until they called Tehran and got instructions."

Adds Phillips: "Bush administration officials only saw what they wanted to see and heard what they wanted to hear -- until the truth became painfully obvious." When it did, it led directly to the decision, announced in February 2003, that the United States would not support the creation of a provisional government for Iraq, for fear that it would give too much power to the Shia Islamists. But it was too late: The war was only weeks away.

As the war and its aftermath unfolded, the United States was clearly and massively outclassed by Iran. Wrote Allawi:

Iran's knowledge of Iraq was all-encompassing and unsurpassed. To the legion of its people with first-hand experience in Iraq, Iran had a number in its upper leadership echelons who were actually Iraqi by birth. A number of senior commanders of the Iranian Revolutionary Guards, the Pasdaran, including a deputy commander, were born and raised in Iraq … Thousands of Iraqis were recruited into the intelligence gathering network of Iran, thus affording Iran the detailed, on the ground information base that would allow it to further refine its policies and tactics.

Thousands of SCIRI fighters crossed into Iraq in 2003. "Border control was nonexistent," says Wayne White. "The Iranians could just drive across. Our analyst in Amarah said it was the talk of the town. But no one could do anything about it. They'd come in convoys, 10 trucks at a time." SCIRI militiamen took up key positions in cities across the south, and the al-Hakims returned to Iraq in a triumphal procession to Najaf.

Meanwhile, in Baghdad, SCIRI took the leading position in Shia circles, greatly aided by the U.S. occupation authorities, who brought Abdul-Aziz al-Hakim and Adel Abdul-Mahdi of SCIRI into a succession of Iraqi governments.

Before long, SCIRI and Badr became widely known for running death squads and torture prisons, often through their control of Iraq's interior ministry. Hakim used the Bolshevik-like discipline of SCIRI to seize control of the United Iraqi Alliance, the Shia coalition that included Dawa, the Sadrists, Fadhila, and Shia independents. Hakim and Abdul-Mahdi became favored interlocutors for the White House, the State Department, and the U.S. military. After the December 2005 elections for a permanent government, the United States favored SCIRI's Abdul-Mahdi for prime minister -- and, according to some accounts, still does. Last December, Hakim made a high-profile visit to meet President Bush -- yet, just weeks later, U.S. forces raided Hakim's compound in Baghdad and arrested three commanders of Iran's Revolutionary Guard.

Those who met with Hakim during that visit painted him as supremely confident of his power and clearly unwilling to make the concessions for power sharing with the Sunnis that are the minimal basis for ending Iraq's civil war. "I was invited to this breakfast with him," says Judith Yaphe, a former CIA expert on Iraq. "He was extremely smug, extremely arrogant. He was very, very sure of himself. And it was right after he'd met at the White House."

In fact, the United States has no option -- if indeed it wants to end the civil war and begin withdrawing its forces -- but to make a deal with Iran, which holds most of the cards. Iran's influence extends far beyond SCIRI, its closest ally. Dawa, parts of which remain closely allied to Iran, cannot move too far from Tehran, in part because it has no militia of its own. Ayatollah Ali Sistani may not share Iran's view of the clergy's role in government, but he's still part of the old boys' club that unites the mullahs of Najaf and Qom, and Iran and Sistani have agreed all along on the importance of cementing the Shia hold on power in Iraq.

Ali Allawi, a participant in several of Iraq's post-Saddam governments, says: "If the Shia are going to retreat from their dominance into a power-sharing role with the Sunnis, they can only do that if they are pressured into it by Iran. The United States has not been able to succeed in that. But the Iranians may."

The result will be a very different Iraq from the one envisioned by the war's planners. "One of the ironies of George Bush's administration is that he has reversed 500 years of Iraqi politics," says Riedel, the former CIA officer. "Five hundred years ago the Ottoman Turks took Iraq, and they put the Sunnis on top. He's reversed that, and in the process he has re-created the Persian Safavid Empire, which lost Baghdad to the Ottomans in 1516. I don't think he had a clue that that's what he was doing in 2003."

Research for this article was supported by The Nation Institute Investigative Fund.