Retired Gen. James Cartwright arrives at U.S. District Court in Washington, Oct. 17, 2016. (Photo: Pablo Martinez Monsivais/AP)

James “Hoss” Cartwright was known as President Obama’s favorite general — a savvy Marine Corps veteran who, as vice chair of the Joint Chiefs of Staff, paid regular visits to the White House providing key advice on everything from drone strikes to the new era of cyber warfare.

But Monday, in an extraordinary rebuke, he stood stiffly in civilian clothes before a federal judge and pled guilty to a felony charge that he lied to the FBI about disclosing classified information to two journalists. It was the latest in an unprecedented series of leak-related cases brought by the Obama Justice Department. It prompted the New York Times (the main beneficiary of Cartwright’s leak, which concerned American cyberwar efforts against the Iranian nuclear program) to denounce his prosecution as “chilling.”

“Are you under the influence of any drugs, narcotics” or alcohol that might “cloud your judgment?” said U.S. Judge Richard Leon, using the standard language asked of all criminal defendants, as he briskly grilled the retired four-star general about his decision to enter a guilty plea.

Cartwright, 67, with his lawyer, former White House counsel Gregory Craig, standing beside him, responded with barely audible monosyllables: “No, sir,” he said in response to the question about being on drugs. “Yes, sir,” he told Leon, when asked if he fully understood the charge against him and that it might send him to federal prison.

Cartwright’s plea caps a four-year-long leak investigation over disclosures in a book and article by New York Times reporter David Sanger about how the U.S. and Israel unleashed a computer virus known as “Stuxnet” to disable Iranian nuclear centrifuges. He also pled to lying about disclosures he made to former Newsweek editor Daniel Klaidman about the administration’s covert efforts to disrupt the Iranian nuclear program. Klaidman is now deputy editor of Yahoo News.

Cartwright is the 10th person to be criminally charged under President Obama in a case related to classified disclosures — more by far than were brought by any president before him. Critics have charged Obama, who once promised the “most transparent administration in history,” with conducting a “war on whistleblowers” meant to discourage government employees from disclosing government abuse and misconduct.

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But the Cartwright case may have been the most sensitive leak investigation of all. It appeared from the start to involve what is known in Washington as a politically authorized leak. It revealed Obama’s direct role in authorizing aggressive covert action against the Iranian regime that, as White House aides spun it, avoided a military confrontation with that country yet still achieved the U.S. government’s goal of thwarting Tehran’s nuclear ambitions.

Moreover, the information Cartwright is said to have disclosed appeared in a news story and book that came out in June 2012 — smack in the middle of an election year when the White House was intent on burnishing the president’s national security credentials in his reelection campaign against Mitt Romney.

According to details disclosed in federal court today, Cartwright spoke to New York Times reporter Sanger on multiple occasions between January 2012 and June 2012, and those talks included discussions about what a federal prosecutor described as “top secret classified information.”

In early June, 2012, Sanger’s book about Obama’s foreign policy, “Confront and Conceal,” appeared, along with a front page New York Times story that included bombshell details about the White House’s role in the Stuxnet attack. Under the headline, “Obama Order Sped Up Wave of Cyberattacks Against Iran,” the Times article disclosed the president’s direct participation in the decisions to unleash Stuxnet — complete with details from inside White House situation room meetings, in which Cartwright participated. It reported how the Iranians were “mystified” and “confused” by the cyberattacks. It quoted one American official describing the “brilliant” malicious code injected into Iranian computers. Another “senior administration official” appeared to be gloating about how involved the president was in directing the effort: “From his first days in office, [Obama] was deep into every step in slowing the Iranian program — the diplomacy, the sanctions, every major decision,” the unnamed senior official is quoted as saying. “And it’s safe to say that whatever other activity might have been under way was no exception to that rule.”

But Republicans were up in arms, accusing the Obama White House of leaking some of the most sensitive classified information in the government’s possession — including American collaboration with the Israeli government in the cyberattack — to help the president get reelected. They demanded the appointment of a special prosecutor — and then Attorney General Eric Holder acceded, naming U.S. attorney Rod Rosenstein of the Maryland office (a Bush White House holdover) to investigate the Stuxnet leak.

Shortly thereafter, a federal grand jury was empaneled and top White House aides — including former national security advisor Thomas Donilon and chief of staff Denis McDonough — were hiring lawyers. But the FBI, armed with an email trail between Sanger and Cartwright, settled on the Marine Corps veteran (who had retired from the U.S. military in August 2011 but still held a top secret security clearance and sat on the Defense Policy Board, as well as serving on the board of directors of Raytheon, a top defense contractor.) In November 2012, FBI agents interviewed Cartwright and, shown a list of quotes and statements from Sanger’s book — “a number of which contained classified information” — he denied being the source of any of them, according to a criminal information entered into the court record today. Cartwright also denied discussing what is referred to as “Country 1” — a reference to Iran — with Klaidman.

By early January 2013, Cartwright knew he was in trouble and resigned from the Defense Policy Board, citing health reasons and the “press of business.” In June of that year, NBC News first reported that Cartwright was the target of the leak investigation.

But the investigation dragged on for three more years, in part because of the highly sensitive subject matter, information that the U.S. intelligence community (and White House officials) were loathe to confirm. At one point, informed sources tell Yahoo News, the State Department and the White House even asked the Justice Department to delay the case until after the U.S.-Iranian nuclear agreement was finalized, fearing that a public confirmation of Stuxnet (and the U.S. collaboration with the Israelis) would jeopardize the negotiations.

In the end, special counsel Rosenstein and Justice Department lawyers chose to thread the needle, charging Cartwright only with making false statements to the FBI about what he told Sanger and Klaidman, but avoiding any reference to the nature of the classified information he disclosed and confirmed. For his part, Cartwright has told friends what many expected would be a major part of his defense: He only spoke to the journalists in the first place because it was his “understanding” the White House wanted him to — in part to wave them off false (and potentially damaging) classified details from another source. It was a defense he appeared to allude to in a statement released today.

“It was wrong for me to mislead the FBI on November 2, 2012, and I accept full responsibility for this,” Cartwright said. “I knew I was not the source of the story and I didn’t want to be blamed for the leak. My only goal in talking to the reporters was to protect American interests and lives; I love my country and continue to this day to do everything I can to defend it.”

In his own statement, his lawyer, Craig, portrayed what his client did as part of the way things work in Washington: “In his conversations with these two reporters, Gen. Cartwright was engaged in a well-known and understood practice of attempting to save national secrets, not disclosing classified information,” he said. “His effort to prevent publication of information that might harm American lives or national security does not constitute a violation of any law.”

Neither Cartwright nor Craig explained how the information the general confirmed “saved” American lives. How that defense will play with Judge Leon, a former Republican Capitol Hill staffer appointed by President George W. Bush, is not clear. Cartwright faces a maximum of five years in prison. Under a deal worked out with prosecutors, the government won’t recommend more than six months. Craig will argue for no jail time at all, and according to sources close to Cartwright, push for a pardon before President Obama leaves office. The judge set sentencing for Jan. 17 — three days before the end of the president’s term.

Meanwhile, the New York Times portrayed the case as another blow to press freedom. Without confirming that Cartwright was Sanger’s source and asserting he relied on “multiple sources in Washington, Europe, the Middle East and elsewhere,” a spokesperson for the Times said the reporting the Times journalist did for the Stuxnet story “serves a vital public interest: explaining how the United States is using a powerful new technology against its adversaries and the concern that it raises about how similar weapons can be used against the U.S. We will continue to pursue that reporting vigorously.”

“We are disappointed that the Justice Department has gone forward with the leak investigation that led to today’s guilty plea by Gen. Cartwright,” the paper’s spokesperson said. “These investigations send a chilling message to all government employees that they should not speak to reporters. The inevitable result is that the American public is deprived of information that it needs to know.”

Klaidman declined comment.