Rice, who once traveled the globe as America’s top diplomat, found herself describing another type of diplomacy to a federal court jury: the Bush administration’s effort in 2003 to kill a New York Times story that threatened to reveal a CIA effort to undermine Iran’s nuclear program by secretly providing Tehran with flawed plans for an atomic weapon.

Rice told jurors that she was acting on the direct orders of President George W. Bush when she asked the Times not to go forward with the article, written by veteran national security correspondent James Risen.

“The president and I talked about it and decided I should ask the New York Times leadership to come to the White House for a meeting to discuss why that story should not be published,” Rice said during her nearly 45-minute stint Thursday afternoon at the trial of ex-CIA officer Jeffrey Sterling in Alexandria, Virginia.

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“I certainly understood the [implications] of the White House asking the New York Times not to publish a story. That’s why I talked first to the president about whether we should even do so,” Rice added.

Rice said she was gravely concerned when she heard the Times had gotten wind of the closely guarded CIA program, which involved a Russian nuclear engineer working with the spy agency to try to entice the Iranians into adopting designs altered by scientists at a U.S. national laboratory.

“It was one of the only levers that we believed we had — that the president had — to try to disrupt the Iranian nuclear program,” the former secretary of state and national security adviser said.

Talking points used by Rice at an April 2003 meeting with Risen and the then-chief of the Times’ Washington Bureau, Jill Abramson, show Rice didn’t hold back when describing the cataclysmic consequences that could flow from publishing the story.

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“This information in the wrong hands could easily lead to the death of a U.S. citizen and conceivably contribute to the deaths of millions of innocent victims of a foreign nuclear weapons program,” Rice said, according to the talking points. She told jurors she hewed closely to the script but could not be sure she delivered them verbatim.

Rice also confirmed that at the meeting held in her office and attended by then-Director of Central Intelligence George Tenet she asked the Times not only to withhold the story but to cease reporting on it and to get rid of all documents relating to it.

“I asked if they had any materials, they would destroy them,” said Rice, who was serving as national security adviser at the time. “I knew they wouldn’t give them back to us.”

The Times ultimately declined to run the story. However, Risen published it three years later in his book “State of War.”

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After the book was published, the FBI stepped up a criminal investigation into the leak. Sterling, one of several former CIA handlers for the Russian engineer at the center of the operation, was indicted in 2010 on charges that he leaked details of the operation to Risen. The ex-CIA officer faces 10 felony counts, including unauthorized disclosure of national defense information, mail fraud and obstruction of justice.

Rice, now a professor at Stanford and a fellow at the Hoover Institution, was calm and composed during her time on the witness stand. However, she was notably more cooperative with the prosecution than with the defense.

Prosecutors appeared intent on using Rice’s testimony to establish the lengths to which the government had gone to prevent the story from getting out and to underscore for jurors that the information was so potentially damaging to U.S. national security that the Times declined to run it.

However, the prosecution initially said it preferred to avoid imposing the inconvenience of testifying on Rice and instead sought simply to show jurors the talking points she read at the 2003 meeting with the Times.

U.S. District Court Judge Leonie Brinkema rejected that proposal.

Abramson said in an interview broadcast last year that she regretted the decision to kill Risen’s story.

“It seemed, in the calculus of all of the major stories we were dealing with at that point, not worth it to me and I regret that decision now,” she told “60 Minutes.” “I regret that I did not back a great reporter, Jim Risen, who I’ve worked with and who then worked for me and whose work I knew was solid as a rock.”

The government has argued to jurors that, in fact, Risen’s reporting was not so solid. Prosecutors contend that he relayed Sterling’s claims that the program was botched because the errors inserted in the nuclear designs were so obvious that the Russian felt compelled to alert the Iranians to them. Risen also suggested that the CIA operation could actually have contributed to Iran’s nuclear program.

CIA officials and prosecutors contend the operation was not mismanaged or botched and that the flaws embedded in the designs were never discovered by the Russian engineer or by Sterling. Instead, the officials say the Russian flagged the Iranians — with CIA consent — to missing elements in the designs. That part of the operation was designed to prolong contact with the Iranians and to elicit more intelligence about their program, officials said.

The former secretary of state answered the prosecution’s questions directly Thursday, albeit almost always in full sentences that repeated much of the relevant query. But during relatively brief cross-examination by the defense, she tended not to answer the questions directly in the first instance and responded instead with a thought of her own on the subject. She usually answered the original question on the second or third attempt.

The defense didn’t appear to score any major blows against Rice or even to try to do so, but it did expose some potential discrepancies in her account.

While the CIA’s former spokesman wrote in an e-mail at the time that Rice had previously gone to Risen’s editors to kill another story, Rice said she had no recollection of such an event prior to the 2003 showdown with the Times over Risen’s Iran nuclear story.

Rice also couldn’t recall telling the FBI that there were two main ways to kill a story: tell a news organization that the story was accurate and too dangerous to report or tell the outlet that it was inaccurate. “I don’t remember that specific statement,” she said

And Rice said with the passage of time she couldn’t remember the presence at the meeting of the CIA spokesman, Bill Harlow, and a top CIA official, Stephen Kappes. Nor could she recall what Tenet told Risen and Abramson in response to the Times’s reporting that the operation had been botched.

“It was a very long time ago,” she said. “I don’t recall what Dr. Tenet said.”

The prosecution asserts that Sterling lied to Risen and congressional aides about the program in order to damage the CIA’s reputation because the CIA officer, who’s African American, was angry at the spy agency for refusing to settle a racial discrimination lawsuit he had filed. The suit was eventually dismissed after the government asserted that litigating it would divulge state secrets.

The defense is arguing that information in Risen’s book could have come from a variety of people, including the Russian engineer, one of Sterling’s supervisors at the CIA and congressional aides. Sterling’s lawyers also say the government has no direct evidence of their client’s guilt and is asking jurors to convict based on mere “supposition” that Sterling leaked to Risen.

Rice’s attendance in court drew a near-capacity crowd of onlookers to that public gallery. She swept into the courtroom just before 3 p.m., accompanied by an entourage of about 10 people, at least one of whom appeared to be a bodyguard. Jurors seemed to listen intently as she testified and to understand her significance in the Bush era.

When prosecutor Eric Olshan asked if the national security adviser was “a high-ranking government position,” Rice replied with one of her few smiles on the witness stand: “Yes. I think that’s fair.” Several members of the jury chuckled at the statement.

Nearly all the witnesses who have testified at Sterling’s trial, which got underway Tuesday, have done so from behind a pair of large screens which prevent most of those in the public gallery from seeing the witness. Those screens were removed from the courtroom Thursday just before Harlow and Rice took the stand.

So far, jurors have heard from a series of CIA officers responsible for handling the Russian engineer, referred to in Risen’s book and in court by the code name Merlin. With the exception of Harlow, the CIA personnel were identified in court solely by their first names and last initials.

Risen’s attempt to fight a subpoena in the case failed, with the courts ultimately refusing to recognize his claims of reporter’s privilege. However, he insisted he would go to jail rather than reveal his sources. Attorney General Eric Holder ultimately decided not to press the issue and prosecutors elected not to call Risen even to confirm the basic accuracy of his book.

The leak trial, the first of its kind to take place in a federal district court in nearly three decades, is expected to conclude by the end of the month.