In July, a group of intelligence analysts at the U.S. military’s Central Command accused their bosses of distorting and selectively editing intelligence reports about the fight against ISIS in order to portray that campaign as more successful than it really was. As a result of those complaints, the Pentagon’s inspector general opened an investigation.

Now, the allegations of misconduct have extended to a possible cover-up, with some analysts accusing the senior intelligence officials at CENTCOM, Maj. Gen. Steven Grove and his civilian deputy, Gregory Ryckman, of deleting emails and files from computer systems before the inspector general could examine them, three individuals familiar with the investigation told The Daily Beast.

One U.S. official said the alleged activity could amount to obstruction and interference with the inspector general’s investigation, which began last summer. He noted that files relevant to the investigation began to disappear from CENTCOM computers after the Pentagon watchdog’s staff began their work.

Two sources said that investigators are piecing together a trail of emails and reports to find out what may have been deleted, as well as what officials outside CENTCOM knew about potential manipulation of intelligence.

The analysts themselves have taken steps to preserve material that could be used as evidence, these people said.

All three individuals spoke on condition of anonymity because they were not authorized to discuss the investigation publicly.

The inspector general has been examining emails and other documents contained on CENTCOM’s computers and interviewing staff at the command, in Tampa, Florida, multiple sources had said previously.

But the allegations of a cover-up underscored the degree to which intelligence analysts have essentially mounted an insurrection aimed at correcting what they see as unprofessional behavior by their own leaders.

Grove, Ryckman, and other CENTCOM higher-ups are named in the complaint to the inspector general, which is said to be extensive and written in a harsh, critical tone, according to those familiar with its contents.

In interviews, several individuals have described CENTCOM as having a “toxic climate,” in which Grove in particular created an expectation: Those who toe the official, upbeat line about the fight against ISIS are rewarded, while those who don’t are marginalized.

“The cancer was within the senior level of the intelligence command,” one defense official told The Daily Beast.

A former senior U.S. intelligence official who has worked with Grove described him as hard-charging and demanding of his analysts, but said he had no reason to suspect the general would make up information or fabricate reports.

It was unclear whether the inspector general is looking into allegations that Grove and Ryckman destroyed documents. A spokeswoman for the IG declined to comment beyond an initial statement in September, which acknowledged that an investigation was underway and focused on CENTCOM’s intelligence directorate, or J2, which Grove runs.

“The investigation will address whether there was any falsification, distortion, delay, suppression, or improper modification of intelligence information; any deviations from appropriate process, procedures, or internal controls regarding the intelligence analysis; and personal accountability for any misconduct or failure to follow established processes,” the statement said.

On Monday, Rep. Devin Nunes, the chairman of the House Intelligence Committee, sent a letter to the inspector general inquiring whether emails and other documents had been deleted, and requesting copies of any material that may have been found on CENTCOM computers, according to a congressional official.

The New York Times reported last week that military officials had told Congress that some email and documents may have been deleted before they were turned over to investigators, citing a senior congressional official, and said that current and former officials have made similar claims.

At the heart of the analysts’ allegations is what they describe as a persistent effort by Grove and his team to downplay or even change reports that that questioned how much progress a U.S.-led coalition is making in the Obama administration’s stated goal to degrade, destroy, and defeat ISIS.

Draft reports that contained a more pessimistic view, or that questioned the efficacy of hitting certain targets, were sent back to the analysts for more extensive rewriting.

Obama himself weighed in on Sunday about the allegations of doctored intelligence.

“I don’t know what we’ll discover with respect to what was going on in CENTCOM,” Obama said, responding to a report about the investigation in The New York Times. “What I do know is my expectation—which is the highest fidelity to facts, data, the truth.”

The analysts’ concerns about ISIS intelligence being manipulated have their roots in earlier complaints about reports on al Qaeda.

In 2012, U.S. intelligence agencies produced a draft National Intelligence Estimate, which said that al Qaeda no longer posed a direct threat to the U.S. homeland. That assessment, which is supposed to represent the consensus view of all intelligence agencies, was in keeping with the Obama administration’s argument that the terror network had been dealt a massive blow following the death of Osama bin Laden and sustained efforts by the U.S. to dismantle the group and its affiliates.

But, as The Daily Beast previously reported, some officials, most notably then-director of the Defense Intelligence Agency, Gen. Michael Flynn, argued against that reassessment, and had the judgment about al Qaeda no longer posing a direct homeland threat struck from the document.

“Flynn and others at the time made it clear they would not go along with that kind of assessment,” one U.S. intelligence officer who worked on the al Qaeda file told The Daily Beast in 2014. “It was basically: ‘Over my dead body.’”

The analysts now calling foul on doctored ISIS reports have also noted the past experience with al Qaeda assessments in the complaint to the inspector general, said two sources familiar with its contents.

One of those people said that while the al Qaeda history is not a front-and-center issue, it’s part of the background material that goes to support the analysts’ broader argument that some intelligence leaders are hostile to analysis that runs counter to the White House’s public statements.