WASHINGTON -- Mark Phillips wanted out of the spy business. He was so fed up with petty intrigue that some days he imagined walking out of his windowless office and never coming back.
Then, one morning last January, the veteran polygrapher who handled national security clearances got an assignment that would upend his life. "This is a PRIORITY special request," the paperwork read. "Make a thorough assessment of subject's mental health."
The orders contradicted everything he'd been taught about the ethical and legal limits of polygraphing. Phillips refused to do it.
His decision that day pitted him against a secretive and little-known U.S. agency and prompted him to accuse his bosses of illegally prying into Americans' private lives.
The agency has a different view. The National Reconnaissance Office sees Phillips as a malcontent who took matters into his own hands for questionable reasons.
McClatchy pulled together the story of the internal struggle based on interviews with Phillips and Chuck Hinshaw, a former colleague who also was troubled by the polygraph practices. The account also draws from interviews with more than a dozen others in the usually secretive polygraph world and hundreds of agency documents, including performance reviews, policy papers and memos in which the agency argues its case.
Their dispute is unfolding as the Obama administration moves aggressively to prosecute self-proclaimed whistleblowers, asserting that they're endangering national security by revealing the government's secrets.
The National Reconnaissance Office declined to respond to McClatchy's questions, saying only that its polygraph program "is in compliance with the law."
When Phillips joined the agency at the end of 2009, he already had worked for a long list of spy agencies over two decades.
But even in intelligence circles, the secrecy at the National Reconnaissance Office was impressive. Created in 1961 as the keeper of spy satellites, it was one of the last federal agencies to be acknowledged by the U.S. government.
Its classified budget is estimated to be $10 billion a year. Even so, it didn't have its own staff. It relied on employees loaned from the Air Force and the CIA, creating an unusual union between the military and a spy agency.
An Air Force civilian and former Marine, Phillips saw his job of polygraphing applicants and employees as largely straightforward. He was supposed to ask them about spying, terrorism and the disclosure of classified information.
His bosses, however, seemed to think otherwise.
"We are not only testing to catch 'spies,' " his supervisor wrote to him after one of his polygraphs. "As security officers we have a responsibility that drives us to actively search out any and all violations and concerns an individual may have coming into the room."
Phillips wondered what that meant. In the intelligence world, Congress permitted only the CIA and the National Security Agency to use such broad polygraph tests to decide whether to give clearances. In so-called "lifestyle" polygraphs, those two agencies could ask a host of personal questions, including about crimes, psychological problems and financial troubles.
Hinshaw, a National Reconnaissance Office polygrapher since 2005, also noticed the difference from other agencies. But he saw his job as a balancing act. He first tried to establish rapport and then move to root out a secret.
Hinshaw's bosses considered him good at what he did. By 2008, the agency had made Hinshaw an acting supervisor. Like other well-regarded polygraphers there, he received thousands of dollars in bonuses for the confessions he collected.
The office began pushing its polygraphers to extract as many confessions as possible. Every four months, supervisors showed them their confession rates. The agency also posted each polygrapher's numbers internally for everyone to see. It praised polygraphers who had high rates or coaxed out especially shocking confessions.
The routine, however, began to worry some polygraphers. They were being told to collect much more intimate information about people than they thought was legal. Some of them voiced their objections. "You guys are killing me with all these emails," a supervisor told them.
In June 2011, the supervisor set up training for the "elicitation" of such details. A group of veteran polygraphers again complained to their supervisors. Everyone is confused, they said. If we have the authority to do what we're doing, show us. The supervisors maintained that everything they were doing was legal.
Hinshaw left the meeting unsettled. He once had reassured himself that he'd never crossed the line. He began to wonder whether that was really true.
Later that year, Hinshaw's supervisor handed him a file with unusual instructions: "Don't show this to anyone."
It was a request for a prohibited lifestyle polygraph.
When Hinshaw asked whether it was allowed, he was told not to worry. So he tried not to. He did the test and the contractor passed.
But the special requests continued.
One morning, a middle-aged woman came in for a standard counterintelligence polygraph.
The contract employee had passed the National Reconnaissance Office's polygraph almost 15 years before. But after she'd taken the job, she applied to the CIA. During the CIA's test, she admitted that she'd smoked pot once in the last four years.
Hinshaw asked her about her drug use in passing. But she denied smoking pot since, so he moved on. He posed the usual counterintelligence questions. She passed without a problem. He sent the file on expecting to never see it again.
Soon afterward, his supervisors approached him with questions about his approach. Why hadn't he pursued the drug issue? She could be hiding more.
They decided to bring her back for a second polygraph session. The test, known as a specific issue polygraph, would seek more information about her possible drug use. Policies required them to be specific to one topic, not a fishing expedition.
But no matter how Hinshaw approached the question, she wouldn't confess to further drug use.
"Come on," he thought. "Admit it."
As he continued to probe, his instinct told him she was hiding something else, perhaps another secret related to drug use. He knew that at other agencies he would have let it go. But now he nudged her more.
Finally, she hinted at something she didn't want to talk about. Slowly, it came out. One relative was a "terrible man." She mentioned something he'd done to her when she was 16 years old.
"There were other girls," she told Hinshaw. She began sobbing.
Hinshaw then realized: She'd been molested.
"I understand," he told her.
She looked at him through tears. "Do you?" she asked.
Hinshaw decided it was time to shut it down. He'd gotten all he could.
But his supervisor had another idea. He demanded that Hinshaw continue the questioning: "Go back in there and get details."
By then, the questioning had gone on almost four hours.
"You don't understand," he told them. "This woman needs help."
Three supervisors continued to pressure him. If you don't go, we'll send someone else in.
Hinshaw worried that another polygrapher would push her over the edge. But he couldn't bring himself to continue. Exhausted and unnerved, he refused. They sent in another polygrapher. But they never got anything more.
Hinshaw thought the agency had gone too far. Polygraphers squeezed every personal secret out of people without regard for the consequences. He questioned whether the government needed to know such details to keep the country safe.
Most people have personal humiliations they don't want anyone to know about. Hinshaw knew that firsthand. He was supposed to tell the agency about financial troubles he was facing. Like many Americans, his house had plummeted in value. He and his wife had decided to proceed to foreclosure.
But he waited to tell the agency. After he eventually did months later, in late 2011, the agency revoked his security clearance, which meant he couldn't work there anymore. The agency thought he no longer could be trusted.
Hinshaw, 45, knew his career was probably over. He also realized he didn't want to return to the National Reconnaissance Office.
Phillips, however, became determined to prove that the agency was wrong. He hunted down its policies and discovered that it had agreed to follow Pentagon polygraph rules.
"I've got them," he thought.
Its test was supposed to be about national security. As a result, all questions were supposed to have a "relevance to the subject of the inquiry," the Pentagon rules said. It shouldn't be pressuring polygraphers to go after personal information, Phillips concluded.
But when he made the same argument to a top agency official, Sharon Durkin, her response surprised him. She asserted that the agency relied on the same legal authorities as the CIA. If that were true, the National Reconnaissance Office had no such limits. Without hesitation, she also confirmed that the agency had authorized lifestyle tests.
Phillips kept pressing. He wrote a memo that went to the agency's attorney. He complained to an Air Force manager. All told, at least 10 officials within the agency and the Pentagon were made aware of his concerns.
Once deemed an "asset to the program," Phillips became known as a troublemaker. He became openly defiant, expressing his criticism in front of supervisors and colleagues. In a meeting with other polygraphers, a supervisor gestured at him and called his questions "a cancer on the program."
The criticism in his annual reviews was more restrained but just as clear.
"Instead of spending time trying to improve his information collection skills, Mr. Phillips has spent an inordinate amount of time documenting, making complaints and arguing why he believes our program is collecting information in violation of (Pentagon) regulations.
"His accusations are without merit."
Top polygraph officials started observing his sessions regularly. He suspected that they wanted to catch him in a mistake. They told him he needed more supervision.
At one point, while conducting a polygraph, he glanced up and saw that a ceiling tile was loose.
"Are they watching me now?" he asked himself.
Phillips excused the job applicant for a break. He climbed up on a chair and looked behind the tile. He stared into a dark and empty hole.
"I've been doing this too long," he thought as he slid the tile back in place.
His bosses began citing him: He was lazy. He was insubordinate. He filed his reports incorrectly. The agency suspended him for three days without pay.
Most importantly, it saw no merit in his complaints.
After a legal review of Phillips' assertions, the agency's assistant general counsel Mark Land concluded in April that the National Reconnaissance Office wasn't illegally pursuing personal information during polygraphs. "Corrective action is not required," he wrote.
After more than two years, Phillips decided he couldn't fight any longer. At the end of May, he resigned. The Pentagon Inspector General's Office now is investigating his complaint of retaliation.
Tish Wells contributed to this article.
By Marisa Taylor