The Iranian scientist executed by his own government after being convicted of spying for the U.S. seemingly was discussed in emails that crossed Hillary Clinton’s private server, fueling Republican accusations about how “reckless” the former secretary of state’s server set-up truly was. 

Iran confirmed Sunday that Shahram Amiri was hanged last week – years after he defected to the U.S.; later returned home, where he was heralded as a hero; and then was tried and convicted of spying for the U.S.

While there are conflicting accounts of Amiri’s odyssey from Iran to the U.S. and back, he did appear in a video in 2010 while living in the U.S. claiming to have been kidnapped by American and Saudi agents. He walked into the Iranian-interests section at the Pakistani Embassy in Washington later that year and demanded to be sent home. 

But there are reports going back years that Amiri, despite his claims to the contrary, was being paid to provide the CIA with information about Iran’s nuclear program.

And, un-redacted Clinton server emails released last year appear to refer to Amiri as “our friend” – though it’s unclear whether those references put him at any additional risk.

An email forwarded to Clinton by senior adviser Jake Sullivan on July 5, 2010 — just 10 days before Amiri returned to Tehran — says: "We have a diplomatic, 'psychological' issue, not a legal one. Our friend has to be given a way out." 

The email by Richard Morningstar, a former State Department special envoy for Eurasian energy, concludes, "Our person won't be able to do anything anyway. If he has to leave, so be it."

Another email, sent by Sullivan on July 12, 2010, appears to obliquely refer to the scientist just hours before his appearance at the Pakistani Embassy became widely known.

"The gentleman ... has apparently gone to his country's interests section because he is unhappy with how much time it has taken to facilitate his departure," Sullivan wrote. "This could lead to problematic news stories in the next 24 hours.”

Sen. Tom Cotton, R-Ark., speaking Sunday on CBS News’ “Face the Nation,” cited those mentions in renewing concerns about Clinton’s server set-up.

“In the emails that were on Hillary Clinton's private server, there were conversations among her senior advisers about this gentleman,” he said. “That goes to show just how reckless and careless her decision was to put that kind of highly classified information a private server.  I think her judgment is not suited to keep this country safe.”

The issue could cause renewed problems for Clinton in the campaign, after the FBI and Justice Department cleared her and decided not to pursue charges over her private email use.

Republican presidential nominee Donald Trump retweeted a story about the email references to the scientist. Trump backer David Clarke, Jr., told Fox News on Monday that the references are “extremely problematic.”

“If people don’t trust you, they’re not going to work with you. … We have to rely on informants,” he said. “The biggest concern of any informant is they don’t want to be outed.”

A Clinton spokesperson pushed back after Cotton’s comments.

"The Trump campaign has never met a conspiracy theory it didn't like. He and his supporters continue to use increasingly desperate rhetoric to attack Hillary Clinton and make absurd accusations because they have no ideas for the American people,” the spokesperson said. “It's pretty remarkable to baselessly claim that Hillary Clinton is responsible for this tragic death." 

The Clinton campaign pointed to a Washington Post column backing up their view. 

A State Department spokeswoman also argued Monday that the execution had nothing to do with the references in the Clinton server emails, since the scientist’s case had already been discussed publicly going back years. 

Amiri was hanged the same week that Tehran executed a group of militants, a year after Iran agreed to a landmark accord to limit uranium enrichment in exchange for the lifting of economic sanctions.

Amiri first vanished in 2009 while on a religious pilgrimage to Muslim holy sites in Saudi Arabia.

In interviews, he later described being kidnapped and held against his will by Saudi and American spies. U.S. officials, though, said he was to receive millions of dollars for his help in understanding Iran's nuclear program.

Iranian judiciary spokesman Gholamhosein Mohseni Ejehi said Amiri "had access to the country's secret and classified information" and "had been linked to our hostile and No. 1 enemy, America, the Great Satan."

The spokesman told journalists that Amiri had been tried in a death-penalty case that was upheld by an appeals court. He did not explain why authorities never announced the conviction, though he said Amiri had access to lawyers.

Hillary Clinton, while she was secretary of state, publicly commented on Amiri’s claims at the time, stressing that Amiri had been in America "of his own free will."

"He is free to go," she had said.

The Associated Press contributed to this report.