The real motive for the scrutiny, Mr. Bigley said, stemmed from complaints Mr. Lovinger made in 2016 about lucrative Pentagon contracts awarded to outside consultants, including at the Office of Net Assessment, the Pentagon’s strategy group where he worked.

Their defense took on its deep-state tinge over the summer after an academic named Stefan Halper, the recipient of one of the contracts Mr. Lovinger had questioned, was identified as an F.B.I. informant who sought information from Trump associates during the early stages of the investigation into ties between the campaign and Russia.

As Mr. Trump and conservative media began to portray Mr. Halper as a deep-state spy inside the Trump campaign, labeling it Spygate, Mr. Bigley amplified his deep-state defense. Though Mr. Lovinger had not known about Mr. Halper’s work for the F.B.I., he had complained about his Pentagon contract.

“Mr. Lovinger was targeted because he blew the whistle on Stefan Halper and a Clinton crony getting suspicious defense contracts,” said Tom Fitton of the conservative watchdog group Judicial Watch, which has sued for files about the case. “It is disturbing that the Defense Department may now be implicated in Spygate targeting of President Trump.”

But there is no evidence Mr. Lovinger’s clearance was revoked for political reasons, said Robert O. Work, the deputy secretary of defense in both the Obama and Trump administrations, asserting the officials who oversaw Mr. Lovinger were fiercely apolitical. “It is quite surprising to me that someone would think this is some sort of deep state,” Mr. Work said.

Mr. Lovinger has found a champion in Representative Louie Gohmert, Republican of Texas, who said this year without evidence that he believed the Justice Department was “spying” on him for his criticism of the Russia inquiry. Mr. Gohmert has introduced a bill, the Adam S. Lovinger Whistleblower Reprisal Act of 2018, aimed at giving additional protections to government employees who report wrongdoing.

A Spreading Strategy

While Mr. Lovinger may have seized on the defense early, it is spreading. Jerome Corsi, who recently published a book called “Killing the Deep State,” employed it as he began publicly discussing his potential plea deal last month with the special counsel overseeing the Russia investigation, Robert S. Mueller III.