WASHINGTON — The deal that freed an American jailed in Cuba and ended 53 years of diplomatic estrangement between the United States and Cuba was blessed at the highest levels of the Holy See but cut in the shadowy netherworld of espionage.
A personal appeal from Pope Francis, American officials said, was critical in persuading Cuba’s president, Raúl Castro, to agree to a prisoner swap and the freeing of the American aid worker Alan P. Gross. The pope, officials said, acted as a “guarantor” that both sides would live up to the terms of a deal reached in secret.
The most tangible breakthrough, however, came almost a year into the talks, when the United States, at loggerheads with Cuba, proposed to swap three Cuban agents jailed in the United States for a Cuban working for American intelligence who had been held in a jail in Cuba for nearly 20 years.
By introducing another figure to the talks — the kind of horse-trading that was standard in Cold War spy swaps — the White House was able to sidestep the appearance that it was trading Cuban spies directly for Mr. Gross. Cuba had sought a straight swap but the United States resisted, saying Mr. Gross had been wrongfully imprisoned.
All told, the negotiations to free Mr. Gross and reopen ties with Cuba took a year and a half. In nine meetings, held in Canada and the Vatican, a tiny circle of aides to Mr. Castro and President Obama hashed out the gritty details as well as grand questions of history.
Looming over their efforts was a mounting fear among the Americans that Mr. Gross’s health was deteriorating. Several months ago, Secretary of State John Kerry warned Cuba’s foreign minister, Bruno Rodríguez Parrilla, that if Mr. Gross died in captivity, all of the administration’s efforts to reopen relations with Cuba would be for naught.
Word of the talks was kept under extraordinarily tight wraps, but in March, Mr. Obama brought in an influential outsider. The president briefed Pope Francis, who was born in Argentina and is the first head of the Roman Catholic church from Latin America, in a one-on-one meeting over a spare desk adorned with a gold crucifix at the Vatican. Days later, the pope wrote letters to Mr. Obama and Mr. Castro, appealing to both to keep pushing for an agreement.
“You just cannot overstate the importance of this pope,” said a senior administration official, speaking on condition of anonymity to discuss the negotiations. “This pope, coming from the region, has a resonance with leaders in the region, including Cuba.”
Graphic | How America’s Relationship With Cuba Will ChangeWhich travel and trade restrictions will be eased or eliminated.
Obama’s First Move
The seeds of this week’s opening were laid soon after Mr. Obama took office in 2009, when he loosened restrictions on the ability of Cuban-Americans to visit relatives and send money to their families there. In April 2009, Mr. Obama told a gathering of Western Hemisphere leaders that the United States sought “a new beginning with Cuba.”
But the thaw quickly froze again in December 2009 when Mr. Gross, a contractor for the United States Agency for International Development, was arrested and accused of crimes against the Cuban state for bringing telecommunications equipment into the country. The State Department began a long, fruitless campaign for his release.
Hillary Rodham Clinton described her failure to win Mr. Gross’s freedom as one of her major regrets as secretary of state. But as she prepared to leave the State Department, she nevertheless wrote a memo to Mr. Obama urging him to reconsider the trade embargo against Cuba.
Slide Show | A Decades-Long Thaw in U.S.-Cuba Relations A look at Cuba’s fraught relationship with the United States since its 1959 revolution.
The president had been leaning in the same direction, officials said, and when he and his aides laid out their foreign-policy priorities for the second term, they put Cuba near the top. When the Cuban government loosened some restrictions on travel for its citizens, Mr. Obama decided the time was right to make a higher-level diplomatic overture.
To spearhead the effort, he chose two young aides: Benjamin J. Rhodes, a deputy national security adviser and speechwriter, and Ricardo Zuniga, a Cuba expert of Honduran descent, who is the National Security Council’s senior director for Western Hemisphere affairs. Mr. Zuniga, who had worked at the American Interests Section in Havana, was recruited to the White House to help with such an effort, a senior official said, while Mr. Rhodes had been involved in the White House’s opening to Myanmar.
For months, the two men took commercial flights to Canada to meet with an only slightly larger delegation from Cuba, a senior official said. The meetings usually lasted a day but sometimes stretched to a second day.
A Canadian government official, who was not authorized to speak publicly, said Canada arranged locations in Toronto and in Ottawa for about seven meetings. Canada did not participate in the talks.
“I don’t want to exaggerate Canada’s role,” Prime Minister Stephen Harper told the Canadian Broadcasting Corporation. “But look, I’m pleased the president acknowledged our role in this.”
What Cuba Wanted
In the early stages of the talks, officials said, it was not clear to the Americans what the Cuban government most wanted. Was it an end to American-sponsored pro-democracy programs? Did Cuba want to be taken off the State Department’s list of state sponsors of terrorism? Or was it the release of the Cuban Five, five Cuban intelligence officers convicted of espionage and, in one case, murder?
The Cuban negotiators, for example, repeatedly objected to the American military prison at Guantánamo Bay.
In earlier negotiations, the Americans had played down Mr. Gross’s importance, calculating that this would increase the odds that the Cubans would release him after he was sentenced and had lost his appeal. Plus, after two of the Cuban Five were paroled, American officials hoped that the Cubans would release Mr. Gross on humanitarian grounds.
The first member of the Cuban Five, Rene González, was released in 2011 after serving 13 years of his sentence. He was required to serve three years of probation in the United States, but in 2013, a judge decided he could stay in Cuba after he went there for his father’s funeral if he renounced his United States citizenship. A second member of the Cuban Five, Fernando González, was released early in 2014 and was deported.
Yet the Cubans still would not release Mr. Gross. As the talks dragged on through 2013, it became clear to the American delegation that getting the remaining three members of the Cuban Five back was a top priority for the Cuban government — a point made clear in Mr. Castro’s statement on Wednesday, which hailed the prisoners as heroes.
At that point, the American side tabled the notion of a straight spy swap and proposed that the three remaining members of the Cuban Five be exchanged for a Cuban who had worked for American intelligence. It would be part of a broader move toward the normalization of relations in which Mr. Gross would be set free as a humanitarian gesture.
“When we raised this intelligence asset,” a senior official said, “that was not something the Cubans anticipated.”
American intelligence officials have said little about the Cuban agent, except that he was instrumental in exposing and disrupting a ring of Cuban operatives in the United States that included members of the Cuban Five. A senior American official identified him as Rolando Sarraf Trujillo. Multiple news accounts in recent years have identified Mr. Trujillo as a former Cuban intelligence officer who has been in prison in Cuba since 1995.
While Mr. Kerry was not involved in the secret channel in Canada, he played an important role in reinforcing the White House’s message. As the chairman of the Senate Foreign Relations Committee, Mr. Kerry had come to know Mr. Parrilla, Cuba’s foreign minister. That gave the United States another channel to deliver messages to the Cuban authorities.
In phone calls with Mr. Parrilla — Mr. Kerry held four of them last summer — he delivered a stark message: If any harm came to Mr. Gross, the entire deal would be off. Mr. Gross’s mother was in declining health, and the Americans were afraid if she died, his condition might deteriorate or he might even harm himself. After Evelyn Gross died last summer, Mr. Kerry sent him a handwritten letter urging him not to lose faith.
Mr. Kerry also reassured lawmakers on Capitol Hill, who were concerned that the administration was not doing enough to free Mr. Gross. At one meeting with his former Senate colleagues, he said, “Guys, trust me: We could have a backchannel cooking to bring Alan home and do something bold, and you wouldn’t know and you couldn’t know.”
Mr. Kerry cited similar secret negotiations between the United States and Iran held in the Persian Gulf state of Oman, which paved the way for an interim agreement on the Iranian nuclear program. Officials said Mr. Kerry viewed the opening to Cuba much like the opening to Vietnam, in which he played a role as a senator and a Vietnam veteran.
The Presidents Meet
Even as the two sides were talking, there was an impromptu meeting of Mr. Obama and Mr. Castro at the funeral of Nelson Mandela in December. The two men shook hands, though the White House said later that Mr. Obama had not raised Mr. Gross’s plight with Mr. Castro.
The Vatican’s role predated Pope Francis. One of his predecessors, Pope John Paul II, visited Cuba in 1998, and the church remains hugely influential among Cubans. The Obama administration first sought to enlist the Vatican’s support when Pope Benedict XVI was in office. It worked even more actively with the Vatican after Pope Francis came to the Vatican in 2013.
The pope’s new secretary of state, Cardinal Pietro Parolin, an Italian, had served as papal nuncio in Venezuela and was well versed in Latin America politics. Mr. Kerry was also in contact with Cardinal Parolin, meeting him at the Vatican in June and again a week ago.
The Cuban government could not afford to ignore the church’s influence, and the Vatican used it, including to persuade the Cuban negotiations to go along with the idea of a prisoner swap.
“It was less a matter of breaking some substantive logjam but more the confidence of having an external party we could rely on,” said a senior official, speaking on condition of anonymity to discuss the negotiations. “This was a very complicated piece of business.”
In October, as negotiations reached a critical phase, the Vatican hosted a meeting of American and Cuban negotiators, in which they sealed the final terms of the agreement. On Nov. 6, two days after the midterm elections, Mr. Obama convened a meeting of his National Security Council to sign off on the new policy.
Still, the two delegations met one more time in Canada to work out the logistical details of the swap. Those details were complicated: Representative Chris Van Hollen, a Maryland Democrat who was part of a delegation sent to pick up Mr. Gross in Havana, said their blue-and-white government plane was not allowed to take off for Washington until five minutes after the plane carrying the Cuban prisoners landed on Cuban soil.
Ian Austen contributed reporting from Toronto, and Julie Hirschfeld Davis contributed reporting from Washington.
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