They wanted him dead.

For years, a clandestine U.S. intelligence team had tracked a man they knew was high in the leadership of al Qaeda — an operative some believed had a hand in plotting the gruesome 2009 suicide attack in Afghanistan that killed seven CIA officers.

Their pursuit was personal, and by early 2014, according to a source directly involved in the operation, the agency had the target under tight drone surveillance. “We literally had a bead on this guy’s head and just needed authorization from Washington to pull the trigger,” said the source.

Then something unexpected happened. While agents waited for the green light, the al Qaeda operative’s name, as well as information about the CIA’s classified surveillance and plan to kill him in Pakistan, suddenly appeared in the U.S. press.

Abdullah al-Shami, it turned out, was an American citizen, and President Obama and his national security advisers were torn over whether the benefits of killing him would outweigh the political and civil liberties backlash that was sure to follow.

In interviews with several current and former officials, the al-Shami case was cited as an example of what critics say was the Obama White House’s troublesome tendency to mishandle some of the nation’s most delicate intelligence — especially regarding the Middle East — by leaking classified information in an attempt to sway public opinion on sensitive matters.

By the end of Mr. Obama’s second term, according to sources who spoke anonymously with The Washington Times, the practices of leaking, ignoring and twisting intelligence for political gain were ingrained in how the administration conducted national security policy.

Those criticisms have resurfaced in the debate over whether overall intelligence fumbling by the Obama White House in its final months may have amplified the damage wrought by suspected Russian meddling in the U.S. presidential election last year.

On repeated occasions during the Obama era, high-level sources and some lawmakers lamented to The Washington Times, the president’s inner circle ignored classified briefings and twisted intelligence to fit political goals. Long before Donald Trump appeared on the White House campaign scene, many pointed to an incident during the 2012 election cycle as the most dramatic evidence of how that approach affected the handling of national security threats.

‘Understating the threat’

On the campaign trail in 2012, Mr. Obama declared that al Qaeda was “on the run,” despite a flow of intelligence showing that the terrorist group was metastasizing — a circumstance that led to the rise of the Islamic State.

Many Americans believed the president was justifiably touting a major success of his first term with the U.S. Special Forces killing of al Qaeda founder Osama bin Laden in 2011. But the gulf between Mr. Obama’s campaign pronouncements and classified briefings provided to Congress touched off a heated debate in intelligence circles over whether the president was twisting the facts for political gain.

“Candidate Obama was understating the threat,” then-House Permanent Select Committee on Intelligence Committee Chairman Mike Rogers told The Times in an interview after the 2012 election. “To say the core [was] decimated and therefore we [had] al Qaeda on the run was not consistent with the overall intelligence assessment at the time.”

Reflecting back this month, Mr. Rogers suggested that Mr. Obama — like many presidents before him — had a propensity for pushing certain politically advantageous narratives even if they contradicted classified intelligence.

Indeed, controversy has long swirled around politicized intelligence and leaks. The George W. Bush administration was accused of “stovepiping” intelligence it needed for its case to invade Iraq in 2003 while ignoring bits that may have undercut the rationale for war.

That case blossomed into a major scandal known as the “Plame affair.” White House staffer Scooter Libby was convicted of lying to investigators about the leak of the name of covert CIA officer Valerie Plame, whose husband had challenged the administration’s claims about Iraq’s weapons of mass destruction. President Bush later commuted Mr. Libby’s sentence.

With regard to the Obama White House, Mr. Rogers told The Times, the circumstances were different but no less disturbing. “Over the course of their time in office, the Obama administration’s world got smaller and smaller,” said the Michigan Republican, who retired from Congress in 2015. “They listened to fewer and fewer different opinions. When you do that, that is how you miss things.”

‘Heart was never in it’

Chaos and instability in the Middle East factored into one Obama-era intelligence leak that officials now say badly undermined national security.

The CIA’s covert “Train and Equip” program was crafted to aid forces seeking to overthrow Syrian President Bashar Assad after the 2011 Arab Spring protests exploded into a civil war in Syria.

Train and Equip began with a flow of “nonlethal aid” to certain Syrian rebel groups, but as its budget ballooned to some $1 billion, the program morphed into an unwieldy and ineffective effort to assist an unconventional military campaign.

One former senior intelligence official said the program was badly undermined because the White House was constantly leaking details of efforts to build a Free Syrian Army with cash, weapons and intelligence.

“Obama had drawn a red line on Syria over chemical weapons, but then he didn’t do [expletive],” the former official told The Times. “The White House was facing a lot of political pressure to show they had policy for Syria, so they leaked the CIA’s covert action plan. They leaked it for purely political reasons, so they could say, ‘Look, look, we have a Syria strategy.’”

Kenneth Pollack, a former CIA analyst now with the conservative American Enterprise Institute think tank in Washington, said other factors also undermined any chance for the program to succeed. Mr. Obama and his top aides were openly wary of being dragged deeper into the Syrian fight while the administration was trying to execute a strategic “pivot to Asia” — away from the heavy U.S. foreign policy focus on the Middle East.

“Obama’s heart was never in it, and the administration wanted nothing to do with it,” Mr. Pollack told The Times. “He mostly did it to avoid domestic political blowback. We could have done so much more, but the way it was run, it killed itself.”

Mr. Pollack, who once worked in the Clinton White House, said the program’s recruitment vetting was ridiculous. “The [Obama] administration more or less insisted, ‘We will only accept applicants … who had never met a jihadist.’ The vetting standards were absurd and excluded almost everyone who had any contact with the opposition in Syria,” Mr. Pollack said.

“It was like they thought we were going to wage a civil war against the Assad government with members of the social pages of The New York Times,” he said. “The Harvard crew team was not going to show up.”

In the long run, the policy’s failure provided a clear window for Iran and Russia to expand their military presence and political influence into the power vacuum created by Syria’s war.

‘Unmasking’

And then there was unmasking.

Controversy has swirled for the past year around the Obama administration’s use of a process that allowed high-level White House officials to learn the redacted identities of Americans swept up in classified surveillance against suspected foreign operatives during the months surrounding the presidential election.

For decades, national security officials at the highest level have used their security clearances to engage in the process known as “unmasking” while reading raw intercepts from around the world for better understanding of relationships that might impact America’s safety.

President Carter’s hawkish national security adviser, Zbigniew Brzezinski, was known by America’s spies as one who “loved raw intelligence,” according to Bob Woodward’s book “Veil, The Secret Wars of the CIA, 1981-1987.”

“Unmasking itself is not nefarious or conspiratorial; it’s done all the time around the world by ambassadors and CIA station chiefs,” said one former CIA clandestine service officer who spoke with The Times. “It’s a standard procedure and involves a rigorous and bureaucratic process … to ensure whoever’s seeking the unmasking of names has a legitimate reason.”

But Republicans believe the process — and the safeguards against abuse — went terribly awry in the final months of the bitter campaign between Mr. Trump and Democrat Hillary Clinton and through the transition period between Mr. Trump’s unexpected victory and inauguration.

Remarks by former Trump National Security Adviser Michael Flynn, as well as Mr. Trump’s son-in-law, Jared Kushner, and former top White House strategist Steve Bannon, were all captured in surveillance of a Trump Tower meeting in December 2016. Susan E. Rice, Mr. Obama’s national security adviser, has since acknowledged she asked that the identities of the Americans in the surveillance be revealed, citing what she said were legitimate concerns about the purpose of the group’s meeting with foreigners.

Although the unmasking itself may have been justified, the former CIA clandestine service officer said, what came next was dangerous.

“The issue is when any names that have been unmasked end up getting leaked to the press,” the former officer said. “And that is certainly what looks like happened vis-a-vis the Obama administration’s unmasking of Trump officials who were in meetings with Russians or Turks that were under American intelligence surveillance.”

Rep. Devin Nunes, California Republican and chairman of the House intelligence committee, has gone further, suggesting that Obama administration officials strategically leaked the names to smear Mr. Trump and fuel a narrative that the Trump campaign was secretly working with foreign forces.

‘Come on, Mr. President’

Suspicion that the Obama White House intentionally leaked the unmasked names has been fueled by what intelligence sources say was the administration track record of other sensitive leaks — which stretched back to the Abdullah al-Shami case in Afghanistan.

CIA agents were shocked when their classified drone surveillance against al-Shami suddenly appeared in 2014 reports by The Associated Press and The New York Times, one intelligence source told The Washington Times. “There’s no question this guy got wind of the reports,” said the source. “The leak gave him a heads-up, and he suddenly disappeared. We lost our bead on him.”

Some at the CIA were outraged. Agents had been tracking the al Qaeda operative since early 2009, believing he had been directly involved in a bomb attack that injured several officials at U.S. Forward Operating Base Chapman in Afghanistan. Al-Shami’s fingerprints turned up on packing tape around a second bomb that didn’t explode.

Roughly a year later, there was another attack on Chapman, a key clandestine operations center in Afghanistan, in which seven CIA officers were killed. Some suspected al-Shami played a role in that attack as well.

But as badly as the CIA wanted al-Shami dead, the case carried controversial legal questions.

Abdullah al-Shami — Arabic for “Abdullah the Syrian” — was the nom de guerre of a young man named Muhanad Mahmoud al-Farekh. Although raised in Dubai, al-Farekh was an American citizen because he was born in Texas.

By the time the CIA had him in its crosshairs in 2014, Mr. Obama was reeling from the furor sparked by his authorization of a drone strike in 2011 that killed another American citizen: al Qaeda propagandist Anwar al-Awlaki in Yemen.

The American Civil Liberties Union condemned the al-Awlaki strike as a violation of U.S. law because al-Awlaki had “never been charged with any crime” in an American court.

Fearful of a similar reaction, the Obama administration decided the best course of action would be to leak information about the al-Shami case to stir up public awareness of the conundrum facing the president, the former intelligence officials said.

“Look,” said the source, “I actually appreciate that Obama didn’t like the idea of killing another American without due process. But was leaking this stuff really the right way to handle this?

“I mean, come on Mr. President, it’s your finger on the trigger. You’re the one who decides. All we do is aim the gun,” said the source, who said it was fortunate that al-Shami was later captured alive and secretly flown to the United States for trial.

The al Qaeda operative was convicted in September in U.S. federal court in New York on terrorism charges under his birth name, Muhanad Mahmoud al-Farekh.

The 31-year-old is slated to be sentenced next month.

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