A Trump-supporting Pentagon analyst was stripped of his security clearance by Obama-appointed officials after he complained of questionable government contracts to Stefan Halper, the FBI informant who spied on the Trump presidential campaign.

Adam Lovinger, a 12-year strategist in the Pentagon’s Office of Net Assessment, complained to his bosses about Halper contracts in the fall of 2016, his attorney, Sean M. Bigley, told The Washington Times.

On May 1, 2017, his superiors yanked his security clearance and relegated him to clerical chores.

Mr. Bigley filed a complaint July 18 with the Pentagon’s senior ethics official, charging that Mr. Lovinger’s superiors misused the security clearance process to punish him. He said his client complained about excessive “sweetheart” deals for Mr. Halper and for a “best friend” of Chelsea Clinton.

“As it turns out, one of the two contractors Mr. Lovinger explicitly warned his ONA superiors about misusing in 2016 was none other than Mr. Halper,” Mr. Bigley wrote in his ethics complaint, which called the contracts “cronyism and corruption.”

Mr. Lovinger filed a whistleblower reprisal complaint in May with the Defense Department inspector general against James Baker, director of the Office of Net Assessment. The complaint also singles out Washington Headquarters Services, a Pentagon support agency that awarded the Halper contracts totaling hundreds of thousands of dollars.

In an internal October 2016 email to higher-ups, Mr. Lovinger wrote of “the moral hazard associated with the Washington Headquarters Services contracting with Stefan Halper,” the complaint said. It said Mr. Baker hired Mr. Halper to “conduct foreign relations,” a job that should be confined to government officials.

“It was a topic of conversation within the office,” Mr. Bigley told The Times. “What is Halper doing, and why is he being paid astronomically more than others similarly situated?”

The Office of Net Assessment conducts analyses of future threats and ways to defeat them.

“Nobody in the office seemed to know what Halper was doing for his money,” Mr. Bigley said. “Adam said Jim Baker, the director, kept Halper’s contracts very close to the vest. And nobody seemed to have any idea what he was doing at the time. He subcontracted out a good chunk of it to other academics. He would compile them all and then collect the balance as his fee as a middleman. That was very unusual.”

Mr. Bigley told The Times that the inspector general’s criminal investigative division has interviewed Mr. Lovinger about Office of Net Assessment contracting.

In all, Mr. Lovinger has four cases pending: whistleblower reprisal, criminal division, an ethics complaint and an appeal on his security clearance revocation.

A spokesman told The Times that the Pentagon would not comment on the case’s merits.

The spokesman said the Department of Defense Consolidated Adjudicaitons Facility reviewed Mr. Lovinger’s clearance.

It then “issued a statement of reasons stating why, under [federal guidelines] it would not be clearly consistent with the national interest to continue Mr. Lovinger’s security clearance, and he was provided with the opportunity to respond to the security concerns,” the spokesman said. “After considering all available information, the CAF issued an unfavorable clearance determination and Mr. Lovinger’s clearance was revoked.”

Mr. Bigley said the conflict is that the consolidated authority resides within the Washington Headquarters Services, which is the target of Mr. Lovinger’s complaint.

“The CAF’s entire ‘adjudication’ of this case was orchestrated by corrupt officials at WHS, which was demonstrated numerous times throughout the process,” he said.

To conservatives, Mr. Lovinger is a victim of the “deep state” — Obama loyalists out to harm the Trump administration.

After lodging his complaints about the Office of Net Assessment’s outside research in general and Mr. Halper specifically, Mr. Lovinger sought an assignment to the Trump White House national security staff in January 2017. He was soon confronted with allegations from Mr. Baker that he failed to follow security rules. Mr. Lovinger denies any wrongdoing.

Mr. Baker was appointed chief of the Office of Net Assessment in 2015 by Defense Secretary Ashton Carter, Mr. Obama’s appointee.

The Washington Headquarters Services, which revoked Mr. Lovinger’s clearance, is headed by Barbara Westgate, who was appointed in 2016.

Perhaps the most intriguing narrative in the Lovinger story is the appearance of Mr. Halper, a national security consultant in the U.S. and Britain who is tied to that country’s MI6 spy agency through his business partner.

‘Derivative’ contractor studies

Press reports identified Mr. Halper as a paid FBI confidential human source, whose mission was to make contacts with Trump campaign workers. The FBI was investigating any Trump ties to Moscow at a time when its intelligence officers were hacking Democratic Party computers.

The Daily Caller website documented Mr. Halper’s outreach to George Papadopoulos, a Trump campaign volunteer. He also contacted another volunteer, Carter Page.

According to USASpending.gov, Mr. Halper was paid $411,000 by Washington Headquarters Services on Sept. 26, 2016, for a contract that ran until this March. Mr. Bigley argues that since Washington Headquarters Services awarded the contracts, it should be removed from Mr. Lovinger’s appeal process as the final arbiter.

Mr. Halper paid Mr. Papadoupolos $3,000 for an energy research project the same month he was awarded the $411,000 Pentagon contract.

Mr. Bigley said Mr. Baker initiated the Lovinger inquiry and picked two investigators who the attorney said had no training. Based on their report, Ms. Westgate suspended his clearance.

Mr. Bigley said his client also complained internally about a string of contracts totaling $11 million to D.C. consulting firm Long Term Strategy Group. It is headed by Jacqueline Newmyer Deal, a self-described “best friend” of Chelsea Clinton.

In the fall of 2016, as the election loomed, Mr. Lovinger sent emails to Mr. Baker and other officials at the Office of Net Assessment complaining about the entire outside contracting process. He also said the office failed to write papers on long-term threats presented by radical Islam, China and Iran.

In September 2016, he sent an email to Mr. Baker summing up the perceived problem.

“Some of our contractors distribute to others their ONA work for personal and professional self-promotion,” Mr. Lovinger wrote. “Another part is the growing narrative that ONA’s most high-profile contractors are known for getting paid a lot to do rather peripheral work.

“On the issue of pay, our contractors boast about how much they get paid from ONA. Such boasting, of course, generates jealously among those outside the club, and particularly from those who have tried to secure ONA contracts unsuccessfully.”

He also said: “On the issue of quality, more than once I have heard our contractor studies labeled ‘derivative,’ ‘college-level’ and based heavily on secondary sources. One of our contractor studies was literally cut and pasted from a World Bank report that I just happened to have read the week before reading the contractor study itself. Even the font was the same.”

The Washington Free Beacon in October reported that Hillary Clinton, as secretary of state in 2009, arranged meetings between Ms. Deal and Pentagon officials to discuss contracts.

Ms. Deal said in a statement that no award “resulted directly or indirectly from the actions or influence of Secretary Clinton.”

The think tank said: “Jacqueline Deal and the Long Term Strategy Group (LTSG) are justifiably proud of their collaboration with the U.S. Department of Defense across multiple administrations over the last two decades, beginning under the administration of President George W. Bush. LTSG’s work has consistently earned the highest respect and confidence of its clientele in government and has won LTSG a reputation for producing research and analysis of exceptional quality.”

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