Iran secretly passed to the White House beginning in late 2009 the names of prisoners it wanted released from U.S. custody, part of a wish list to test President Barack Obama’s commitment to improving ties and a move that set off years of clandestine dispatches that helped open the door to nuclear negotiations.

The secret messages, via an envoy sent by the Sultan of Oman, also included a request to blacklist opposition groups hostile to Iran and increase U.S. visas for Iranian students, according to officials familiar with the matter. The U.S. eventually acceded to some of the requests, these officials said, including help with the release of four Iranians detained in the U.S. and U.K.: two convicted arms smugglers, a retired senior diplomat and a prominent scientist convicted of illegal exports to Iran.

The exchanges through 2013 helped build the foundation for the first direct talks between the two nations since the 1979 Islamic revolution, current and former U.S. officials involved in the diplomacy said.

Clandestine meetings between U.S. and Iranian officials that started three years ago in Oman’s capital, Muscat, have yielded negotiations that aim to curb Iran’s nuclear program in exchange for removal of international sanctions. Negotiations here on a final agreement will continue past Tuesday’s deadline, officials said Sunday.

“Oman played a key role in facilitating the back channel between the United States and Iran that helped lead to the diplomacy taking place right now on the nuclear issue,” said Marie Harf, a senior adviser for strategic communications at the State Department.

With a deal in sight, some worry the U.S. will give up too much without getting significant concessions in return. The Obama administration initially called for an end to Tehran’s nuclear fuel production, a dismantling of many of its facilities and a rollback of its missile program—goals that have been dropped.

The long-term impact of a nuclear deal on U.S.-Iranian relations and the broader Middle East is still under debate at the White House.

Some U.S. officials say an accord could moderate Tehran’s revolutionary government and reopen it to the West. Iranian President Hasan Rouhani took office in 2013 pledging to integrate his country into the global economy and ease its repressive political system. Mr. Rouhani has championed nuclear diplomacy, and some U.S. officials say he will be strengthened politically by a deal.

Others in the Obama administration, and leaders in Israel and the Arab states, see the deal as a payoff—Tehran temporarily curbs its nuclear work in exchange for the lifting of sanctions. Mr. Obama has said Iran could recoup as much as $150 billion in frozen assets in the months after a deal.

A reconstruction of the past six years of U.S.-Iranian diplomacy, based on exclusive interviews with officials directly involved from the U.S., Europe and the Middle East, offers supporting evidence for both views.

Seeking an advantage
Tehran has repeatedly used its exchanges with the U.S. to barter for tactical and monetary gains, said U.S. and Arab officials briefed on the talks.

In July 2009, for example, Iran arrested three American hikers on espionage charges after they had inadvertently crossed into Iran from Iraq. Tehran then amplified demands for the release of its own citizens from U.S. jails, including those on the wish list, current and former U.S. officials said. Iran continues to hold at least three other Americans, including a Washington Post reporter.

Iranian officials involved in the nuclear talks have fixated on gaining immediate sanctions relief, U.S. and European officials said, underscoring the quid pro quo nature of the diplomacy.

“The Iran deal was never really about the transformation of the regime or its behavior,” said Aaron David Miller, a former State Department envoy now at the Woodrow Wilson Center for International Scholars. “It was always a transactional deal to avoid war, buy time, defuse the nuclear issue and test the possibility, however remote, that Iran might be enlisted as a partner.”

Over the past six years, U.S. allies in the Mideast say, Iran has expanded its influence in Syria, Iraq and Yemen. Now, they say, Tehran is set to maintain much of its nuclear infrastructure, while scoring an economic windfall.

“This agreement might backfire,” said Yuval Steinitz, Israel’s energy minister, who voiced concern that releasing Iran from sanctions would mean more money flowing into “destabilizing activities in the region.”

White House proponents of the deal, on the other hand, said the past six years of engagement has reduced tensions and opened the door to possible cooperation in the future—against Islamic State, for example. The proposed deal would cap Iran’s nuclear program for at least a decade, allow aggressive facility inspections and reduce Tehran’s stockpile of nuclear materials, they said.

Mr. Obama entered office in 2009 committed to addressing the Iranian nuclear threat through diplomacy rather than military force, current and former U.S. officials said. He sent letters calling for talks to Iran’s most powerful official, Supreme Leader AyatollahAli Khamenei. Mr. Obama dialed down Washington’s rhetorical attacks. And in a Persian New Year’s message to the Iranian people that March, Mr. Obama referred to their country as the “Islamic Republic of Iran,” the first U.S. president to do so.

Mr. Khamenei had a lukewarm response, according to former U.S. officials who saw one of the cleric’s written messages. Then Oman’s U.K.-educated monarch, Sultan Qaboos bin Said al Said, secretly offered to help the White House establish a back channel with Iran. Oman and Iran have long-standing cultural and financial ties.

An early step was the presentation by Tehran to the White House, via Oman, of the confidence-building steps, said officials briefed on the matter. The list was aimed at addressing Mr. Khamenei’s long-held belief that the U.S. sought to overthrow his regime, according to two people who viewed it.

In November 2010, the State Department sanctioned a Pakistan-based militant group, called Jundullah, which had attacked Shiite mosques and military installations in eastern Iran, killing hundreds.

Iranian officials, including Mr. Khamenei, had accused the Central Intelligence Agency of supporting the organization, which Washington denied. Blacklisting Jundullah was a way to confront a terrorist organization and signal positive intentions by the White House, current and former U.S. officials said.

“We wanted to say, ‘If there’s openness on your part, there’s openness on ours,’” said a former senior administration official involved in the decision.

The Iranians also raised concerns about two opposition groups, a pro-monarchy organization based in Los Angeles, called Tondar, and the Mujahedin-e Khalq, which the U.S. had already designated a terrorist organization at the time. The administration didn’t respond to that request, current and former U.S. officials said.

But Iranian students eventually got a break. In September 2011, then-Secretary of State Hillary Clinton announced a “virtual embassy,” allowing Iran to facilitate visas and student-exchange programs. Iranians had complained, via Oman, that U.S. universities were discriminating against their students.

U.S. officials said they didn’t see the move as a favor to Tehran; it could increase pressure on Mr. Khamenei by exposing young Iranians to the West. “The United States has no argument with you,” Mrs. Clinton said in Persian-language TV interviews that month with the British Broadcasting Corp. and Voice of America, targeting Iranians. “We want to support your aspirations.”

While Mr. Obama has been president, the number of Iranian students at U.S. colleges has more than doubled, surpassing 10,000, according to the nonprofit Institute of International Education.

Tehran, meanwhile, increased calls on the U.S. through the Oman channel to release more than a dozen Iranian nationals held in the U.S. and Europe, many on arms-related charges.

A special envoy for Oman’s Sultan Qaboos, a U.S.-educated businessman and diplomat named Salem ben Nasser al Ismaily, brokered the 2011 release of the three American hikers, in part, by paying bonds of nearly $500,000 each. Sultan Qaboos put up the money, U.S. and Arab officials said.

Iranian prisoners
Mr. Ismaily, over the next two years, facilitated the return to Tehran from the U.S. and U.K. of four Iranians prized by their government, these officials said. 

In some cases, the convicted Iranians had served their full sentences, but U.S. authorities worked with Oman to grant them a quick exit. Rather than spending months in immigration detention centers awaiting deportation proceedings, like many foreigners, the U.S. allowed departures within days of their release.

Matthew Kohn, who represented one of the convicted smugglers, Amir Hossein Seirafi,said: “He walked out of prison, and the U.S. Marshals got him on a plane within 48 hours. It was the quickest thing we ever saw.”

Iran also campaigned for the release of Shahrzad Mir Gholikan, who was convicted in 2009 and sentenced to more than five years for illegally exporting night-vision equipment to Iran from Europe. Iranian state TV showed one of the American hikers in custody, Sarah Shourd, posing with Ms. Gholikan’s twin daughters and calling for their mother’s release.

Ms. Gholikan returned to Iran via Oman in August 2012, nearly a year after Ms. Shourd’s release. U.S. officials denied it was a prisoner swap because Ms. Gholikan had served her sentence.

In December 2012, the U.K. government released from house arrest a former Iranian ambassador to Jordan who also had been charged with shipping night-vision equipment to Iran. The U.S. had been seeking to extradite the ambassador, Nosratollah Tajik, for nearly five years on suspicion of illegal exports but ceased its efforts in 2012, current and former U.S. officials said. The Iranian diplomat was among those on the list of prisoners the Iranians sought freed, according to the two officials who viewed it.

A month later, in January 2013, Oman helped expedite the release of Mr. Seirafi, convicted of export violations in 2010. And in April 2013, the U.S. released an Iranian scientist detained in California.

The scientist, Mojtaba Atarodi, was a professor at Tehran’s prestigious Sharif University. The U.S. Treasury Department has sanctioned departments at the school for having alleged roles in developing Iran’s nuclear program.

U.S. authorities arrested Mr. Atarodi in December 2011 when he arrived in Los Angeles but kept his court case sealed. He was convicted of shipping banned items to Iran just days before he returned to Tehran via Oman.

Mr. Kohn, who also represented Mr. Atarodi, said U.S. law-enforcement officials told him of pressure from Iran to resolve the case quickly. “I’d get phone calls from the U.S. attorney’s office where they would say, ‘There is activity around your client, but it’s not coming from us,’” he said. “‘It’s diplomatic activity.’”

Mr. Atarodi told Iranian state media this year that U.S. officials wanted to swap him for one of the Americans held in Iran, Amir Hekmati. “I told them he is a spy, but I have done nothing wrong,” Mr. Atarodi said.

Mr. Hekmati, a former Marine, and his family have denied the espionage charges. He is serving a 10-year sentence in Tehran’s Evin prison for cooperating with an enemy of Iran.

The Obama administration in each of the cases said it wasn’t swapping prisoners. Many of the cases are sealed or partially sealed, restricting comment by many but not all of those involved.

“No one on either side will say there was a formal prisoner swap. But the release of American and Iranian innocent prisoners served as reciprocal ‘goodwill gestures,’” said Joshua Fattal, one of the American hikers, who was freed by Tehran in September 2011.

The return of prisoners on both sides seemed to help build momentum for the secret nuclear negotiations taking place in Oman. An initial meeting between U.S. and Iranian diplomats in July 2012 was largely a failure, participants said.

Over the ensuing year, Iran elected Mr. Rouhani, U.S. sanctions on Tehran tightened and Mr. Khamenei signaled to Oman his commitment to the diplomatic process. In negotiations over the summer and fall of 2013, Iran and the U.S. forged an interim agreement, forming the basis for the final negotiations.

Mr. Khamenei as recently as Tuesday highlighted the role of an international mediator, believed to be Oman, in initiating the nuclear negotiations. But he also signaled his continued skepticism about a deal.

“We told the mediator that we do not trust the Americans and their words, but due to the insistence of that mediator, we agreed to try this issue once more and the negotiations started,” he said in nationally televised speech marking the beginning of the Muslim holy month of Ramadan.

ROAD TO VIENNA
Events in U.S.-Iran Diplomacy

2009 Oman offers to establish secret back-channel between Iran and U.S.

2010-2011 Oman secures release of three American hikers held in Iran

July 2012 U.S. and Iranian diplomats hold first secret talks in Oman’s capital, Muscat

August 2012-April 2013
Four high-value Iranian prisoners returned to Iran from U.S. and U.K. via Oman

September 2013 President Barack Obama holds 15-minute phone call with President Hasan Rouhani

November 2013 Iran and world powers reach interim agreement in Geneva to constrain Tehran’s nuclear program

October 2014 Mr. Obama secretly writes Supreme Leader Ayatollah Ali Khamenei urging cooperation against Islamic State, if nuclear issue resolved

April 2015 Iran and world powers agree in Lausanne on the parameters of a nuclear agreement

Tuesday Original deadline for reaching accord; talks to continue

This article was published by the Wall Street Journal and may be found here.