Even as several Americans imprisoned by Iran began their journey home Sunday, "other Americans" were still being held by the Islamic Republic, a signal Iran has "not turned the page" on its use of hostages as bargaining chips, a congressional source told Fox News.
A plane carrying Washington Post reporter Jason Rezaian, former U.S. Marine Amir Hekmati and Pastor Saeed Abedini landed in Geneva on Sunday evening and were then flown to Germany on a U.S. jet. It is unclear how long the group will remain in Germany.
It is unclear if Nosratollah Khosravi-Roodsari, another freed American, was onboard. The U.S. said he was not, but Iran said he had left the Islamic Republic on the plane. The discrepancy could not immediately be reconciled.
The Americans were exchanged for seven Iranian nationals.
"Those who wished to depart Iran have left," according to a senior U.S. official, speaking on condition of anonymity because of the sensitivity of the matter and privacy concerns for the families.
A congressional source told Fox News the deal was not officially a swap because "innocent Americans held against their will" were exchanged for Iranian nationals, "some convicted of federal crimes." Members of Congress have asked the Justice Department whether the Iranians are being allowed to stay in the U.S. or have been asked to leave the country, the source said.
The Post's publisher, Frederick J. Ryan, Jr., said in a statement, "We are relieved that this 545-day nightmare for Jason and his family is finally over.
"It is hard to put into words what our family feels right now," Hekmati's family said in a statement. "But we remain in hopeful anticipation until Amir is in our arms."
Iran celebrated the lifting of stiff economic penalties now that the Islamic Republic has met a critical benchmark as part of the agreement to pull back its nuclear program.
Secretary of State John Kerry said U.S. officials hashed out the prisoner exchange over 11 or 12 meetings with the Iranians. At times, the Americans thought a deal was set, only to get stuck on the details.
After almost constant conversation over the last few days, they finally did settle it.
Kerry said the nuclear agreement provided the key impetus.
Just before Iran's foreign minister, Mohammad Javad Zarif, announced the July 14 accord with his European Union counterpart, Kerry again raised the issue of the detained Americans.
A photograph of him speaking with Zarif and Iranian President Hasan Rouhani's brother, Hossein Fereydoun, captured the moment.
Things progressed significantly by a November meeting in Vienna on Syria's civil war, when, for the first time, Iran was included in the discussions. Kerry and Zarif met on the sidelines of the talks to discuss the prisoners.
"We actually shook hands thinking we had an agreement," Kerry said. "I thought it was done."
But the deal bogged down in Tehran and never went through. "So we went back to work," Kerry said.
He described the negotiations as difficult, especially as the Iranians made what he said were unacceptable demands. Kerry said the United States made it clear that it would not release a hardened criminal such as an accused murderer or someone with a narcotics record.
"For a long time, this didn't move because of the people they were asking for," Kerry recalled. "We said, `No, and no, and no."'
"And believe me, it's hard when somebody says to you, `Hey, you give us this guy, we let them all out.' And you have to say no. And you know you're keeping people in a not very nice place for the next whatever number of months," he said.
"But there have to be an enforcement of our principles and our standards here. And in the end, we came out in the right place on that."
More progress was made by Kerry's meeting with Zarif on Dec. 18 in New York. By then, American and Iranian teams in Geneva were working hard on the details of the swap.
The U.S. was prepared to release individuals who violated nuclear-related sanctions on Iran, Kerry said. By Saturday night, those penalties were no longer in effect.
"In the end, the president made the call," he said.
Talking to reporters in his plane after landing Sunday morning at Andrews Air Force Base, Kerry said he had hoped to meet the returning Americans in Switzerland.
But after the nuclear talks moved to Vienna and dragged on, he decided to send the lead negotiator on the matter, Brett McGurk, and State Department aide Patrick Kennedy, to await the Americans' arrival.
Kerry said one of the last hiccups that delayed the departure of the Americans was an Iranian military official's misunderstanding about Washington Post reporter Jason Rezaian's mother.
The deal specifically permitted her to accompany Rezaian on the flight. After Kerry spoke to Zarif, that problem was solved.
But the various administrative holdups meant that the Swiss crew set to fly the plane ran into a mandatory crew rest. That set back takeoff several hours.
Kerry said the deal and almost simultaneous implementation of the nuclear deal raise the prospects of increased U.S.-Iranian cooperation on other matters.
Zarif, Kerry said, made it clear that if they got the two tasks done, "there are ways to try to translate this and hopefully be constructive in other things. He specifically said Syria and Yemen."
"I put a big, `Who knows?"' on that, Kerry said, but expressed hope.
Kerry said he would remain at work on other Americans still being held in Iran.
The exchange did not cover Siamak Namazi, an Iranian-American businessman who advocated better ties between Iran and the U.S. and who reportedly was arrested in October, or former FBI agent Robert Levinson, who disappeared in Iran in 2007 on an unauthorized CIA mission.
Asked if Levinson was dead or alive, Kerry said, "We have no idea."
The exchange eases a leading irritant as the two countries gingerly explore prospects for a smoother relationship after decades of hostility -- even as they remain sharply at odds on other fronts.
A fifth American, student Matthew Trevithick, was released independently of the larger swap, and already had headed home.
In turn, the U.S. was pardoning or dropping charges against seven Iranians -- six of whom are dual U.S.-Iranian citizens -- accused or convicted of violating U.S. sanctions.
Three were serving prison terms and received a commutation or pardon. Three others were awaiting trial; the last one made a plea agreement.
In addition, the U.S. was dropping drop Interpol "red notices" -- essentially arrest warrants -- on 14 Iranian fugitives it has sought, officials said.
Fox News' Catherine Herridge and The Associated Press contributed to this report.