“Atrocity” is how Tehran’s Iran News described the slaughter. Some Iranian officials believed that the United States had created al-Qaeda as a tool against the Islamic Republic. Conspiratorial-minded officials remained skeptical that such an operation could be conducted without the American government’s knowledge. But the magnitude of the attack as well as the culprits stunned the Iranian government and its populace. “My deep sympathy goes out to the American nation,” said President Mohammad Khatami. “Terrorism is condemned and the world public should identify its roots and its dimensions and should take fundamental steps to eliminate it.” Mourners held a spontaneous candlelight vigil as thousands of people took to the streets of north Tehran chanting, “Death to terrorists.” Iranian soccer fans observed a minute of silence before a match withBahrain. Even Supreme Leader Ayatollah Ali Khamenei condemned the attacks: “Mass killing is wrong, whether it’s in Hiroshima, Bosnia, New York, or Washington.” During Friday prayers at Qom, Ayatollah Ibrahim Amini said that the Iranian people grieved with the relatives of those killed, and the traditional slogan “Death to America” was absent from the crowds’ mantras.

Tehran had mixed emotions about the new administration. President Khatami desperately wanted to improve Iran’s economy. He needed this for political survival, but also to show detractors within the government the tangible benefits from better relations with the West. Bush’s family ties to the oil industry appeared to be a good omen. Rafsanjani believed that pressure from American oil companies might lead to a lifting of the sanctions. Although his father’s assignment as CIA director caused some unease within the Iranian government, many within the Iranian business community hoped the Republicans would be more sympathetic to lifting the sanctions in order to make money for American companies.

If the terrorist attack changed the focus of theU.S.government, it portended a change regarding Iran too. The traditional American antagonist suddenly loomed as a potential ally. “The Iranians seemed shocked by the scale of the attack,” said Richard Armitage. Iran showed no enthusiasm for al-Qaeda or its Sunni-based objectives.

The perpetrators of 9/ 11 were harbored by a fiercely anti-Shia, anti-Iranian Afghan tribal alliance, the Taliban. Iran supported the main opposition group, the Northern Alliance, with close ties to the legendary Afghan resistance fighter who opposed both the Soviets and the Taliban, Ahmad Massoud. In 1998, Iran threatened to invade Afghanistan following the killing of eight Iranian diplomats by Taliban forces when they stormed the city of Mazar-e Sharif in northern Afghanistan. As a result, Iran increased its support for the Northern Alliance and the anti-Taliban forces. In the first half of 1999 alone, thirty-three cargo planes with 380 metric tons of small arms, ammo, and fuel arrived from the eastern Iranian air base of Mashhad to Tajikistan for transport to the Northern Alliance.

Since the late 1990s, the United Nations had sponsored meetings in Geneva with Afghanistan’s neighbors plus the United States and others with an interest in Central Asia to resolve the myriad problems caused by the Afghan civil war and the Taliban’s victory. Iran housed two million Afghan refugees. Afghan opium made its way through Iran’s porous border bound for Iranian cities as well as the streets of Europe. The seventh floor of the Department of State paid little attention to these discussions, which fell under the auspices of the department’s bureau that handled India and Pakistan rather than the Middle East. But the venue placed American and Iranian diplomats in the same room, and after September 11 the State Department saw this informal venue as a means of reaching out to Iran to leverage its access and cooperation with the Northern Alliance in the forthcoming American attack on the Taliban.

“The Iranians had the contacts to help us in Afghanistan, and appeared to be willing to use their influence in a constructive way,” said Flynt Leverett, a CIA officer serving as the director for Middle East affairs at the National Security Council.

Secretary Powell dispatched Ryan Crocker to meet with the Iranians in Geneva. As cover, the Italians and Germany were included to avoid the appearance of direct talks. But in fact, it would be the first face-to-face discussions between the two nations since 1986, during the arms-for-hostages debacle of the Reagan administration.

Discreet and experienced, and fluent in both Arabic and Farsi, Crocker served in some of the most demanding posts of the Middle East. In April 1983, he suffered superficial injuries from flying glass when an Iranian surrogate detonated a car packed with explosives in front of the U.S. embassy in Beirut. He headed the State Department’s Iraq task force following Saddam’s invasion of Kuwait, before returning toLebanonin 1990 as the ambassador. This would be the first of six ambassadorial appointments in the region, including Iraq in 2007 during the height of the violence following the U.S. invasion and Afghanistan during the surge there under President Obama. Crocker knew something about Iran. His first posting as a Foreign Service officer in 1972 was to the American consulate at Khorramshahr in southwestern Iran. A captive of the student protests on American university campuses at the time, Crocker arrived convinced that a leftist revolution would send the shah’s reactionary, authoritarian regime to the “dustbin of history.” He spent two years traveling the countryside, talking to students and labor organizers trying to prove this thesis. “I could not have identified a politicized mullah if I tripped over one. I had no idea of what Khomeini was writing in Najaf,” Crocker recalled, lamenting his own naïveté. With the shah’s overthrow, Crocker realized the inherent problem of looking at another society through one’s own lens. “I learned the important lesson that you need to check your intellectual baggage at the door when you arrive in someone else’s complex society, and Iran is an incredibly complex country.”

Not everyone in the U.S. government agreed about the wisdom of talking to Iran. When Paul Wolfowitz heard of the Crocker mission, he wanted it shut down. John Bolton concurred, seeing it as a reward for bad behavior and distrusting anything coming out of the mouth of an Iranian official. One of the most strident opponents was William Luti, deputy assistant secretary of defense for Near Eastern and South Asian affairs. A retired navy captain who rose to prominence as Newt Gingrich’s military assistant, he’d earned a doctorate from Tufts University with his dissertation on Operation Earnest Will and the escort of Kuwaiti tankers during the 1980s, in which he’d opposed the joint operation led by CENTCOM. “He is an extremely bright guy and a good friend,” said Tony Less, a commander during the tanker war, “but he is very right wing.”

Luti was excitable regarding Iran. He openly advocated regime change rather than what he saw as fruitless talks with a duplicitous nation. Luti had Larry Franklin, a civilian staffer who shared his views, draw up a set of counterpoints against engagement with Iran. “Iran is a hostile nation,”Franklin began in an eight-point diatribe against the Islamic Republic. “Iran mouthed words of condemnation for the September 11 attacks, but actions speak otherwise.” It violated its international obligations, was duplicitous, and actually worked to undermine the Afghan government and fragment the country. “Iran must cease illegal programs and halt its terrorist ways.”

But Powell and Armitage stood firm, and for once Rice herself interjected, concurring that meeting with the Iranians about Afghanistan could be useful. As long as the discussions remained at a low level and did not stray into other areas of U.S.-Iranian relations, the Pentagon acquiesced and raised no strong objections, other than to razz Crocker with a few good-natured jabs for “talking with the enemy” when he departed on a junket with Rumsfeld in Cairo in order to meet with the Iranians.

Crocker supported meeting with the Iranians. “I generally believe in talking to anyone who will talk to you,” he said. “Maybe you will persuade them; maybe you’ll neutralize them; maybe you can just mess with their mind.

The Iranian delegation consisted of three individuals. In an echo of McFarlane, North, and Cave’s talks fifteen years earlier, all the Iranians had strong connections to the Revolutionary Guard commander, Major General Yahya Rahim Safavi, and to the supreme leader. One was a deputy foreign minister and an experienced hand in international political organizations, another a Revolutionary Guard general who had served as Iran’s liaison to the Afghan Northern Alliance. The third man was the most intriguing to the Americans: former Iranian ambassador toAfghanistanand Bosnia-Herzegovina Mohammad Taherian. His career blurred the distinction between diplomat and military officer. During the 1980s, as ambassador inKabul, he had secretly funneled arms to the mujahedeen, when the Reagan administration was engaged in the same activity. A decade later, as ambassador toBosniain the midst of the Balkan civil war, he had funneled Iranian military aid to the Muslims, an operation that included deploying two hundred to three hundred Revolutionary Guardsmen to Central Europe to fight forBosnia. He had also held private meetings with the CIA on opposing the Serbs during his time in Sarajevo, a fact he informed Crocker’s delegation of during one of their lengthy chats.

From the outset the discussions showed promise. During the breakout sessions during the first meeting inGeneva, the Iranians made it clear that they wanted to support theUnited States in Afghanistan. “They were in favor of swift and decisive action, military action by the United Statesagainst the Taliban,” recalled Crocker. A couple of days before the United States launched its attack on Afghanistan, Crocker was having a theoretical discussion with the Iranians on the makeup of the future Afghan government. One of the Iranians rose to his feet and threw some papers on the floor: “None of this matters if we don’t get on with the war!”

A short time later, the Revolutionary Guard general produced a map and pointed out all the Taliban troop locations. “Here’s where you need to concentrate your bombings,” he advised. Crocker immediately passed this back to Washington.

The Iranians repeatedly stressed that the two countries needed to work together. “We have more in common than differences,” they said. They shared the same adversaries—Saddam Hussein and the Taliban—and needed to end thirty years of estrangement and build a new relationship. “The sweep of history and the geopolitics of the Middle East made Iran and the United States natural allies,” Crocker recalled one saying. Crocker remained uncertain whether the Iranians believed this or if anyone in Tehran shared the same opinion.

The two parties met roughly once a month, bouncing between Geneva and Paris. The Germans and Italians dropped out, leaving the Americans and Iranians alone for hours, meeting in hotel lobbies, Crocker’s suite, and at the United Nations special representative for Afghanistan Lakhdar Brahimi’s plush apartment overlooking the Luxemburg Gardens on the Left Bankof the French capital. The discussions were always cordial and professional. Crocker’s instructions from the State Department were not specific; as they were informal talks, no one back in Washington paid too close attention. With this freedom, Crocker and his Iranian counterparts held long, freewheeling conversations that meandered into a wide array of contentious issues, from history, Lebanon, and Iraq to terrorism.

The Americans and Iranians quickly came to common agreement on the need to stabilize Afghanistan and for mutual cooperation on the formation of a post-Taliban government. Militarily, Iran offered the use of its airfields and ports to support the campaign in Afghanistan. While this offer was rejected, theUnited States did accept an Iranian offer to provide sanctuary for downed American pilots. U.S. airmen were told that if they had to bail out, they should do it over Iran and the Iranian air force would provide search and rescue units to retrieve them.

As the discussions progressed, the Iranian delegation proposed expanding the talks. The State Department prepared a comprehensive package of carrots and sticks designed to take advantage of a strategic opening with Iran. The goal would be a normalization of relations between the two antagonists. Armitage viewed this as prudent planning, but he remained doubtful that Iran would acquiesce to the U.S.demands: ending support for Hezbollah and terrorism and respecting democratic principles.

In November, President Khatami arrived in New York for the opening of the United Nations General Assembly, which had been delayed due to the havoc caused by the collapse of the World Trade Center. The Iranians had two requests. Khatami wanted to go to Ground Zero—the site of theTwinTowers—and light a candle and pay his respects. Second, the Iranians recommended bringing additional Revolutionary Guard officers to expand the security dialogue beyond those in Geneva.

The U.S. government refused both requests. A visit by the president of a terrorist nation would not only insult the memory of those killed, a senior Bush administration official wrote; it threatened to undermine the monolithic nature of the war on terrorism, which lumped Iran, Iraq, and Syria all into the same nefarious category.

Newt Gingrich summed the concern up neatly during lunch with Doug Feith and Peter Rodman less than two weeks after the September 11 attacks. The United States needed to maintain a consistent message that the war on terrorism was a broad campaign and did not distinguish the policy rationale behind each terrorist actor. “We confuse Americans, allies, and our enemies when we speak of Iran joining the coalition against terrorism,” the unofficial minister without a portfolio declared.

But the success of Crocker’s meetings set the stage for the next major diplomatic leap in Afghanistan: the Bonn conference in December 2001. In late fall, Powell appointed Ambassador James Dobbins as the American representative for the Afghan opposition. Although Dobbins was planning on retiring after three decades as an American diplomat, he had unique experience in nation building in the Balkans. Dobbins was tasked to work with the United Nations–supervised negotiations with Afghanistan’s neighbors, including Iran, to structure a new post-Taliban government and constitution.

Few within the government objected to Dobbins’s effort. As the United Nations had invited all of Afghanistan’s neighbors, including Iran, it made no sense not to attend a forum in which the United States needed to exert influence, just to avoid the Iranians. “That would have been the policy equivalent of cutting off our nose to spite our face,” recalled Feith.

Dobbins’s discussions remained autonomous from Crocker’s meetings in Geneva. While each knew of the other’s meetings, the coordination between the two centered back in Washington with Marc Grossman, the number three man at the State Department. Unlike Crocker’s limited, secretive meetings, Dobbins wanted a broader-based delegation from within the U.S. government. The White House dispatched Afghan-born Zalmay Khalilzad to Dobbins’s team. Although an administration hawk on Iran, Khalilzad was fluent in Farsi and had a solid grasp of the intricacies of Afghanistan and generally supported Dobbins’s goals.

Meeting in a sprawling guesthouse called the Petersberg, a holdover from the days when the small German town served as the West German capital, Dobbins led the American delegation—including Luti, who had been sent along to keep an eye on Dobbins—to the UN-sponsored conference to formulate a new government forAfghanistan. Javad Zarif headed the Iranian delegation. Prematurely gray, Zarif looked older than his forty-one years. Educated at San Francisco State with his doctorate from the University of Denver, he was a sensible,  savvy diplomat. Quick-witted and erudite, Zarif deftly navigated the greenrooms of the Western news media, providing a public face of a seemingly rational Iranian government. As a pragmatist, he was distrusted by hard-liners inTehran, and the supreme leader tended to prefer diplomats from the Revolutionary Guard, such as those meeting Crocker. But Zarif had the backing of Khatami and was a powerful player in Iranian diplomacy.

The Iranians remained supportive of the dialogue with the United States. Both the hard-line supreme leader and the reformist president Khatami supported the opening, although for different reasons. Khatami viewed this as an opportunity to revive his reform movement and strengthen his power inIran. Ayatollah Khamenei feared the Islamic Republic was next in America’s crosshairs in its war on terrorism. While the United States had two separate tracks with Dobbins and Crocker, Iran tended to shuttle the same individuals between the two Americans. Not surprisingly, the Iranians’ talking points were consistent regardless of which American they happened to be having tea with that day. Both Dobbins and Crocker reported back that Iran wanted to cooperate in Afghanistan.

The evening before the conference convened, Dobbins received a call from the Iranians asking to meet at their hotel. Fearing Luti would try to derail the talks, Dobbins deliberately excluded him and took Khalilzad to meet with Zarif. Khalilzad proved a valuable sidekick both for his language abilities and for his sage advice during the talks with the Iranians. Zarif and Dobbins spent an hour together comparing notes. Both sides agreed on the core issues: the Northern Alliance should provide the nucleus of a new government and Hamid Karzai was an acceptable candidate for the new president.

When Dobbins briefed his American team the next morning on what had been discussed, another hard-liner in Luti’s party, Harold Rhode, who worked for the Defense Department’s Office of Net Assessment and frequently did special tasks for Wolfowitz, “became agitated,” as Dobbins put it mildly in describing the scene. Luti and Rhode strenuously objected to the talks, rejecting the very idea of any limited convergence of interests between theUnited States and Iran. To Dobbins’s relief, both men left Bonn the following day.

Dobbins and Zarif proceeded to hammer out the framework for a new Afghan government. The two men met every morning at ten o’clock for coffee, with the Italians and Germans coming along to provide the fig leaf of multilateral talks. During one of these meetings over tea and cookies, Zarif brought to Dobbins’s attention a major omission in the draft of the final agreement: “The text makes no mention of democratic elections,” Zarif said in his flawless English. “Don’t you think the new Afghan government should be committed to holding democratic elections?”

Dobbins agreed, somewhat embarrassed that the U.S. delegation had not noticed the absence of this obvious basic tenet of American policy and that the Iranians had.

“Further,” Zarif continued, taking obvious pleasure in stealing the customary American themes, “the draft makes no mention of terrorism. Should we not insist that the new Afghan government be committed to cooperating with the international community to combat terrorism?”

The irony of this was not lost on Dobbins. Despite America’s castigation of Iran as a totalitarian, fundamentalist, and terrorist regime, the country opposed both al-Qaeda and the Taliban and was more democratic than many of Washington’s Arab allies in the Middle East, including the two stalwarts, Egypt and Saudi Arabia. It exposed a major flaw in the Bush administration’s evolving war on terrorism: by lumping Iran, Iraq, the Taliban, and al-Qaeda all in the same monolithic camp, the United States lost the opportunity to exploit the natural divisions and open hostility that existed among those grouped under this broad tent of terrorism.

After more than two weeks, the conference concluded. In the final hours, Zarif and the Iranians played a critical role in uniting the disparate Afghan warlords. Zarif’s personal intervention overcame a final hurdle to the apportionment of the ministry positions among the ethnic groups, which had threatened to derail the entire accord. Both Iran and the United States coalesced behind the new president, Hamid Karzai, a pro-American Afghan who had arrived in Kabul on the backs of American special operations forces.

The following month, Dobbins met again with the Iranians during a fund drive for Afghanistan held in Tokyo. Accompanied by Treasury Secretary Paul O’Neill, the United States pledged only about 5 percent of the $5 billion total to support reconstruction in Afghanistan, a paltry sum that irritated Dobbins and attested to the Bush administration’s disinterest in nation building in Afghanistan. By contrast, Iran offered $540 million, twice as much as Washington. Iran understood what the Bush administration did not: with money went influence over allocation of reconstruction funds and influence in the new government. Over the coming years, Iran followed this up with tens of millions of dollars in additional aid, plus a steady stream of bags of cash given directly to Karzai to ensure Iranian influence over the new government. In January 2002, the Iranians sent technicians to restore radio and television service and provided over a billion dollars in assistance. Tehran established regular commercial airline flights into Kabul, greatly expanded exports of commercial goods into the country, and was a leading supplier of humanitarian aid.

While at the conference, former UN high commissioner for refugees Sadako Ogata passed a note to Secretary O’Neill from the Iranians. They were proposing once again to open a formal dialogue with the United States to discuss all issues dividing the two nations. Dobbins and O’Neill dutifully reported this back to Rice and the State Department. “No one evinced any interest,” Dobbins recalled.

Just before the Tokyo summit, the Revolutionary Guard had aided the administration hawks opposed to any dialogue when they tried to smuggle a ship full of weapons to the Palestinians, then in the midst of their second intifada. Some fifty tons of arms were loaded by a lighter from Qeshm Island onto the ship Karine A. Israeli commandos intercepted the ship in the Red Sea. It seems unlikely that hard-liners inTehran were hoping to scuttle the talks with theUnited States; the Revolutionary Guard operation appears to have been more on autopilot, planned well ahead of time.Israel paraded the crates of Iranian-made explosives and rockets before the press. Immediately, during interagency meetings at the White House, both Peter Rodman and Bill Luti touted this as evidence of Iranian support for terrorism and argued that regime change and not accommodation should be administration policy. “It showed once again you could not trustIran and you cannot change a leopard’s spots,” said one former Bush defense official who urged overthrowing the Iranian regime.

* * *

Despite the apparent harmony on Afghanistan, suspicion about al-Qaeda’s presence in Iran reinforced hard-line views inside the U.S.government. As a sidebar to Crocker’s talks in Geneva, James Pavitt, the CIA’s deputy director for operations, met separately with another Iranian delegation, composed of MOIS agents. Pavitt raised concerns about al-Qaeda fleeing across the Afghan border into Iran. The CIA estimated that some five hundred al-Qaeda suspects and their families were in Iran, including Osama bin Laden’s eldest son, Saad, and one of his daughters. The Iranians responded to Pavitt that they did not have enough forces to guard their expansive and lawless border with Afghanistan and that many undesirables crossed into Iran. But they claimed to have arrested many al-Qaeda members and placed others under house arrest. The CIA passed the names of several high-value al-Qaeda members suspected of being in Iran, requesting that they be turned over to the United States. Iran viewed these al-Qaeda captives as important for its own security. They provided valuable insight into the organization that Tehran viewed as a threat to its own security. Holding them also provided insurance against al-Qaeda attacks against Iran. The several hundred al-Qaeda captives and their families were held in varying degrees of confinement, from prison to limited free movements under the supervision of security officials. The Iranians refused to give up anyone from the bin Laden family, but did turn over one highly sought al-Qaeda affiliate to Karzai’s government in Kabul. In return, Iran requested information on those Taliban members responsible for the killing of their diplomats in 1998. Unfortunately, Crocker responded, the United Stateshad no specific information on the culprits and none were in American custody.

To placate the Americans, Javad Zarif flew to New York. He carried photocopies of the passports of more than two hundred al-Qaeda and Taliban fighters held by Iranian authorities, as well as a flowchart of who each of them was and how that fit into the larger network. In return, Zarif requested America’s help in repatriating some of these captives to Saudi Arabia and Egypt, with whom Washington had better diplomatic relations than did Tehran. One of those in custody was a renegade Afghan who opposed both the Taliban and the United States with equal fervor, Gulbuddin Hekmatyar. Zarif agreed to keep Hekmatyar, a brutal cutthroat, under arrest, as long as the United States did not then accuse Iran of harboring terrorists.

Despite these overtures, the U.S. government remained suspicious that Iran knew far more about other al-Qaeda members in its country. “The Iranians were trying to give us the limited modified hangout,” said Armitage, referring to a quote by Richard Nixon during Watergate. “Give a little ankle and let them think we are showing them everything.”

One of those the CIA suspected of being in Iran was Abu Musab al-Zarqawi. The Jordanian had been bankrolled by Osama bin Laden to form his own militia near Herat in western Afghanistan. A cutthroat, al-Zarqawi later participated in beheading hostages and in organizing suicide bombings against U.S. forces in Iraq, until American special operators dropped a laserguided bomb on him in 2006.

Rumors of al-Zarqawi’s presence in Iran persisted in intelligence circles, which nearly led to a secret raid into Iran to kill him in 2002. The U.S. government learned of an upcoming meeting with al-Zarqawi and other al-Qaeda operatives about obtaining chemical or biological weapons. The meeting was to occur near the northern Iranian city of Chalus, in a house only three kilometers from the Caspian Sea. Navy SEALs developed an imaginative plan. A small team would be air-dropped into the water off the coast, and then make its way across the beach to the suspected al-Qaeda meeting house. Once in position, the SEALs would call in an air strike and drop a thousand-pound smart bomb on top of al-Zarqawi.

Joint Chiefs chair Richard Myers briefed President Bush that it would be a ” high-risk” operation. Iranian military forces were nearby, and the SEALs had serious intelligence gaps—lacking both photographs of the attendees and an agent on the ground to update them on the actual time of the meeting. Myers cautioned against the mission, unless they obtained some rock-solid intelligence that spelled out when al-Zarqawi would be at the safe house. The daring raid had captivated the president, and the hawkish Dick Cheney liked the idea of striking simultaneously at both Iran and al-Qaeda. But President Bush reluctantly agreed with the chairman’s concerns that the risks outweighed the gains. It was a wise decision by Bush. While detractors in the administration used Iran’s failure to produce al-Zarqawi as evidence of Tehran’s obstinacy, the man in question was never even in Iran, but in a remote, ungoverned area ofIraq.

Despite the setbacks of the Karine A and detractors within the government, the United States and the Islamic Republic had sustained their most important diplomatic contact in two decades. The shock of terrorism on a grand scale allowed the two rivals to find common ground in remaking the political landscape of a troublesome Afghanistan. Meanwhile, the quick rout of the Taliban and its al-Qaeda parasites meant that Iraq came up next in the queue, even if the decider had not yet ruled on the next war. In early December, CENTCOM commander Tommy Franks flew to Bush’s ranch in Crawford,Texas. After getting a tour of the large spread, Franks updated the president on the invasion plan for Iraq. While Dobbins had hoped his talks would serve as the catalyst for a permanent thaw with Iran, years of suspicion would not be easily overcome. With the neocon grand design about to come to fruition, Iran would not be a partner; instead, it would be part of the nefarious lineup of the “axis of evil.”

Excerpted from The Twilight War: The Secret History of America’s Thirty-Year Conflict with Iran by David Crist.

Copyright 2012 by David Crist.

Reprinted with permission from The Penguin Press.