WASHINGTON >> Early in 2011, after a hectic visit to Yemen, Secretary of State Hillary Clinton landed in the tranquil Arab sultanate of Oman. She was there to talk to Sultan Qaboos bin Said about an idea one of his envoys first pitched to the State Department in the spring of 2009: that Oman serve as a conduit for secret nuclear talks between the United States and Iran.

Clinton agreed to explore the proposal but was dubious that it would go anywhere.

“Even under the best of circumstances,” she wrote later, “this was a long shot.”

It would be 18 months before she took up the sultan on his offer and dispatched a team of diplomats to Oman to meet with the Iranians.

Clinton, however, was not the only prominent American making discreet trips to Oman in those days. Sen. John F. Kerry, then the chairman of the Senate Foreign Relations Committee and later her successor as secretary of state, was holding his own meetings with Qaboos and his trusted emissary, a businessman named Salem ben Nasser al-Ismaily.

Kerry came away convinced that Oman could deliver Iranians who spoke for their top leaders, and he urged President Barack Obama and Clinton to open a back channel.

“Hillary and company were skeptical,” he said in an interview.

The president, on the other hand, was intrigued by the prospect of an Omani channel, twice telephoning the sultan to ask him about it.

“He was genuinely curious about trying to find an out-of-the-box approach to change the dynamic,” Kerry recalled.

The Iran nuclear deal, signed last year after months of direct negotiations with Iranian officials, is likely to be remembered as Obama’s most consequential diplomatic achievement. In Clinton’s campaign to succeed him, she is claiming her share of the credit for it. The multinational sanctions regime that she cobbled together helped pull Iran’s government to the bargaining table. The team she eventually sent to Oman, she likes to say, “set the table” for Kerry’s diplomatic banquet.

But the behind-the-scenes story of Clinton’s role is more complicated than her public account of it. Interviews with more than a dozen current and former administration officials paint a portrait of a highly cautious, ambivalent diplomat, less willing than Obama to take risks to open a dialogue with Iran and increasingly wary of Kerry’s freelance diplomacy. Her decision to send her own team, some officials said, was driven as much by her desire to corral Kerry as to engage the Iranians.

Clinton, who declined to comment for this article, worried that he was promising too much to lure the Iranians to the table — a worry shared by people in the White House. The senator’s aides, meanwhile, suspected that Clinton was content to run out the clock on an opening. At one point, a frustrated Kerry told his chief of staff, David Wade, “If this is going to go anywhere, we have to get people in a room talking.”

Defenders of Clinton say that her distrust of Iran was warranted, and that her success in lining up the sanctions makes her the best candidate to handle the next phase of the relationship: enforcing the nuclear agreement.

“She’s built one coalition that was tremendously effective in imposing sanctions,” said Jake Sullivan, Clinton’s top policy adviser at the State Department, who was a member of the team sent to Oman for the talks. “If it comes to it, she can rally the world to both deter and punish Iran.”

The secret history of the Iran nuclear diplomacy, parts of which have never been reported before, lays bare stark differences between Clinton and Obama, going back to the 2008 campaign, over how to approach one of America’s most intractable foes.

“They shared the same tactic, which was engagement, but they envisioned different endgames,” said Karim Sadjadpour, an expert on Iran at the Carnegie Endowment for International Peace. “The president’s endgame was, ‘I’m a guy who can bridge differences. I’ve bridged races and countries all my life, so I’m going to be able to resolve this.’”

“Clinton had a more cynical view of the endgame,” he continued. “‘We’re going to engage them not because we think they’re going to reciprocate, but because when they rebuff us, it will expose the fact that the problem lies in Tehran, and not in Washington.’”

Leery from the start

Few would have expected Clinton to be in the vanguard of an overture to Iran. During the 2008 campaign, she ridiculed Obama’s pledge to hold talks with Iran’s leaders without preconditions. She warned Iran that if it ever launched a nuclear strike on Israel, the United States would “totally obliterate” it.

Yet the secret channel’s origins go back to her own special adviser on Iran, Dennis B. Ross, who got a visit at the State Department on Memorial Day weekend in 2009 from al-Ismaily. He came bearing a sheet of paper outlining an offer by Iran to negotiate with the Obama administration on a range of issues, including the country’s nuclear program as well as its support for Hezbollah.

As a general rule, Ross said he viewed such proposals “not with a grain of salt, but a small ton of salt.” But he had gotten to know the Omanis through his work on Middle East peace issues in the 1990s, and he knew their ties to the Iranians were genuine. He said he decided to pass along al-Ismaily’s proposal, with a caveat-laden cover memo, to Clinton. She told Ross to keep talking to him.

A few weeks later, the Iranian authorities cracked down brutally on anti-government protesters, dashing al-Ismaily’s hopes to set up a channel and prompting the White House to shift from a strategy of engaging Tehran to one of pressuring it. Clinton lobbied China and other countries in the U.N. Security Council to impose harsh new sanctions on Iran, a step widely seen as a crucial lever against the Iranians.

Around that time, al-Ismaily got another chance to demonstrate his skills as an intermediary. He negotiated the release of three young Americans who had been arrested by Iranian guards while hiking on the border between Iran and Iraqi Kurdistan. Oman paid bail for the three hikers, roughly $500,000 each.

In December 2010, several weeks after the release of the first American, Ross and a senior official on the National Security Council, Puneet Talwar, secretly traveled to Oman to hear from Qaboos himself how he thought a channel could work. They were impressed by what the sultan told them: He had visited the supreme leader of Iran, Ayatollah Ali Khamenei, and was confident of the country’s seriousness in seeking a nuclear deal.

The next January, Clinton stopped in Muscat, the capital of Oman, for her own briefing. She expressed doubts that the Iranians could negotiate in good faith, but she agreed to put it to a test. Obama was more intrigued: He called Qaboos twice over the next few months to ask him about whether he could deliver Iranians who could speak with the authority of the supreme leader. The White House, intent on secrecy, did not disclose the calls.

Leaning forward, then back

Kerry had long nourished the idea of opening lines of communication to Iran, and he saw his chance when he got involved in trying to free the hikers. That put him in contact with the sultan and his emissary. (Al-Ismaily confirmed this account, but declined to speak on the record about his role in the nuclear talks.)

Kerry visited Oman in late 2011 and the first half of 2012, spending hours with the sultan discussing the possibility of secret talks with Iran. He also met with al-Ismaily — sometimes in London and Rome, other times in Washington. Later, in a one-on-one meeting with Obama in the Oval Office, Kerry told him that the only way to test its potential was to meet the Iranians.

The State Department and the National Security Council, however, deliberated for months without making a decision.

In his zeal to jump-start negotiations, Kerry passed several messages to the Iranians through al-Ismaily. The senator was coordinating his talking points with Obama’s national security adviser, Thomas E. Donilon, with whom he had a close relationship. But his aggressive approach alarmed Clinton, as well as people at the White House, several former officials said. They worried that Kerry had promised the Iranians concessions on enriching uranium that the White House was not yet willing to make.

Kerry, these officials said, indicated to the Iranians that the United States would acknowledge, at the outset of the talks, that Iran had a right to enrich uranium for a civil nuclear-energy program. Iran had long demanded that concession, claiming it was guaranteed by the Nuclear Nonproliferation Treaty. But the United States had steadfastly refused, and the Obama administration was, at that moment, debating how and when to relax that position.

Kerry denies ever signaling to Iran that it had a right to enrich.

“We made it crystal clear to them,” he said.

At the same time, he held out to the Iranians the prospect of their having a peaceful nuclear program, and he was dismissive of hard-liners in Israel and the United States who demanded that Iran dismantle its nuclear infrastructure.

In the fragile atmosphere of early 2012, officials said, Kerry’s forward-leaning style came to be viewed as a liability. Clinton and Obama worried that the Iranians would believe Kerry was speaking for the president.

Sometime that spring, Obama decided that it was time for the executive branch to take over the negotiations. Kerry did not protest, believing that he had taken the process as far as a senator could. Three years later in Vienna, as secretary of state, he would lead weeks of grinding talks that produced a final agreement.

After she left the State Department, Clinton diverged from Obama on a central tactical question: whether to impose harsh new sanctions on the Iranians after they elected Hassan Rouhani, who had run for president seeking better relations with the West to ease Iran’s economic isolation. Clinton was swayed by many in Congress, as well as by Prime Minister Benjamin Netanyahu of Israel, who argued Iran was so desperate for a deal that tightening the vise would have extracted better terms.

“She would have squeezed them again,” a person who has worked with her for several years said, “and the only debate is what they would have done.”

Obama feared that ratcheting up the pressure would undercut Rouhani, unravel the sanctions coalition and doom his diplomatic efforts. He persuaded the Senate to hold off on new sanctions. Clinton never made her differences with Obama public, and she has publicly endorsed his nuclear deal, though with more caveats than her former boss.

“It’s not enough just to say yes to this deal,” she declared in October. “We have to say, ‘Yes, and.’ Yes, and we will enforce it with vigor and vigilance. Yes, and we will embed it in a broader strategy to confront Iran’s bad behavior in the region. Yes, and we will begin from Day 1 to set the conditions so Iran knows it will never be able to get a nuclear weapon.”

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