As Brussels remains under virtual lock down due to threats of another Paris-style terror attack, the investigation into the Paris attacks themselves continues to search for suspects, and the debate over how to respond to ISIS in the United States intensifies, a series of reports is raising concerns about whether or not America’s leaders and politicians are getting the information and assessments they need to make the right decisions.

On Saturday, The New York Times reported on a Pentagon investigation into whether or not intelligence estimates regarding ISIS and events over the past year in Syria and Iraq were being painted in an inappropriately optimistic light:

WASHINGTON — When Islamic State fighters overran a string of Iraqi cities last year, analysts at United States Central Command wrote classified assessments for military intelligence officials and policy makers that documented the humiliating retreat of the Iraqi Army. But before the assessments were final, former intelligence officials said, the analysts’ superiors made significant changes.

In the revised documents, the Iraqi Army had not retreated at all. The soldiers had simply “redeployed.”

Such changes are at the heart of an expanding internal Pentagon investigation of Centcom, as Central Command is known, where analysts say that supervisors revised conclusions to mask some of the American military’s failures in training Iraqi troops and beating back the Islamic State. The analysts say supervisors were particularly eager to paint a more optimistic picture of America’s role in the conflict than was warranted.

In recent weeks, the Pentagon inspector general seized a large trove of emails and documents from military servers as it examines the claims, and has added more investigators to the inquiry.

The attacks in Paris last week were a deadly demonstration that the Islamic State, once a group of militants focused on seizing territory in Iraq and Syria, has broadened its focus to attack the West. The electronic files seized in the Pentagon investigation tell the story of the group’s rise, as seen through the eyes of Centcom, which oversees military operations across the Middle East.

The exact content of those documents is unclear and may not become public because so much of the information is classified. But military officials have told Congress that some of those emails and documents may have been deleted before they had to be turned over to investigators, according to a senior congressional official, who requested anonymity to speak about the ongoing inquiry. Current and former officials have separately made similar claims, on condition of anonymity, to The New York Times. Although lawmakers are demanding answers about those claims, it is not clear that the inspector general has been able to verify them. A spokeswoman for the inspector general declined to comment.

Staff members at the House Permanent Select Committee on Intelligence are also poring over years of Centcom intelligence reports and comparing them to assessments from the Central Intelligence Agency, the Defense Intelligence Agency and others. The committee is not just examining reports about Iraq, Syria and the Islamic State, but also about Afghanistan and other areas under Centcom’s purview. The insurrection inside Centcom is an important chapter in the story of how the United States responded to the growing threat from the Islamic State. This past summer, a group of Centcom analysts took concerns about their superiors to the inspector general, saying they had evidence that senior officials had changed intelligence assessments to overstate the progress of American airstrikes against the Islamic State, also known as ISIS.

The analysts said problems in Iraq were rooted in deep political and religious divides that could not easily be solved with a military campaign, current and former officials have said. Yet Centcom’s official posture remained generally upbeat.

It is not clear whether the Centcom assessments significantly changed the Obama administration’s views about ISIS. While Centcom was largely positive about American gains, other agencies have been more pessimistic. The White House has generally been measured in its assessments.

But President Obama and senior intelligence officials have acknowledged that the Islamic State’s rapid emergence caught them by surprise. At the least, the prospect that senior officials intentionally skewed intelligence conclusions has raised questions about how much Mr. Obama, Congress and the public can believe the military’s assessments.

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That investigation was prompted by complaints this past summer from Centcom’s longtime Iraq experts, led by Gregory Hooker, the senior Iraq analyst. In some ways, the team’s criticisms mirror those of a decade ago, when Mr. Hooker wrote a research paper saying the Bush administration, over many analysts’ objections, advocated a small force in Iraq and spent little time planning for what would follow the invasion.

Lawmakers originally said that the Centcom investigation would be completed in weeks. But Pentagon investigators have found the work painstaking and it could span months. In addition to determining whether changes were made to intelligence reports — and if so, who ordered them — the investigators, like the staff members of the House intelligence committee, are studying reports from other intelligence agencies produced at the time to determine what was actually occurring in Iraq and Syria when the reports were written.

Yesterday, the Times reported that the White House had ordered its own investigation into the issue, and the Republican Chairman of the House Intelligence Committee hit on the issue during an interview on Face The Nation:

WASHINGTON, Nov 22 (Reuters) – The Republican chairman of the House of Representatives Intelligence Committee said on Sunday he was concerned that Pentagon intelligence reports on the fight against Islamic State did not reflect a grimmer reality on the ground.

Devin Nunes was asked on CNN about a New York Times report on whether intelligence assessments from U.S. Central Command painted an overly optimistic picture of the fight against Islamic State in Iraq and Syria.

He said members of his committee had long noticed discrepancies between what they saw during visits to the region and the intelligence reports.

“We travel to many of these countries and we meet with the people on the ground and it’s almost all the time, what we hear and see on the ground when we talk to the folks that are actually doing the work, is grimmer than the intelligence reports,” Nunes said on CNN’s “State of the Union.”

“More alarming, what we hear the president and his senior officials saying to the public – it just doesn’t jive with, what they’re saying in public and what we see on the ground,” he said.

Nunes said his committee was working with other congressional panels to study the Centcom intelligence reports.

“We’re trying to gather all the facts,” he said. “We’ve heard from a lot of whistleblowers and other informers.”

While this issue of faulty intelligence, or perhaps what should more properly be called faulty intelligence analysis, has gotten front page attention in the wake of the Paris attacks and the sense of a growing threat from ISIS that extends far beyond Syria and Iraq, it’s not a new story at all. Back in September, for example, The Daily Beast noted more than fifty intelligence analysts affiliated with Central Command had been complaining that their analysis of the ISIS threat was being altered by someone higher up the chain of command:

More than 50 intelligence analysts working out of the U.S. military’s Central Command have formally complained that their reports on ISIS and al Qaeda’s branch in Syria were being inappropriately altered by senior officials, The Daily Beast has learned.

The complaints spurred the Pentagon’s inspector general to open an investigation into the alleged manipulation of intelligence. The fact that so many people complained suggests there are deep-rooted, systemic problems in how the U.S. military command charged with the war against the self-proclaimed Islamic State assesses intelligence.

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

Two senior analysts at CENTCOM signed a written complaint sent to the Defense Department inspector general in July alleging that the reports, some of which were briefed to President Obama, portrayed the terror groups as weaker than the analysts believe they are. The reports were changed by CENTCOM higher-ups to adhere to the administration’s public line that the U.S. is winning the battle against ISIS and al Nusra, al Qaeda’s branch in Syria, the analysts claim.

That complaint was supported by 50 other analysts, some of whom have complained about politicizing of intelligence reports for months. That’s according to 11 individuals who are knowledgeable about the details of the report and who spoke to The Daily Beast on condition of anonymity.

The accusations suggest that a large number of people tracking the inner workings of the terror groups think that their reports are being manipulated to fit a public narrative. The allegations echoed charges that political appointees and senior officials cherry-picked intelligence about Iraq’s supposed weapons program in 2002 and 2003.

The two signatories to the complaint were described as the ones formally lodging it, and the additional analysts are willing and able to back up the substance of the allegations with concrete examples.

Some of those CENTCOM analysts described the sizeable cadre of protesting analysts as a “revolt” by intelligence professionals who are paid to give their honest assessment, based on facts, and not to be influenced by national-level policy. The analysts have accused senior-level leaders, including the director of intelligence and his deputy in CENTCOM, of changing their analyses to be more in line with the Obama administration’s public contention that the fight against ISIS and al Qaeda is making progress. The analysts take a more pessimistic view about how military efforts to destroy the groups are going.

The large number of analysts who complained to the Pentagon inspector general hasn’t been previously reported. Some of them are assigned to work at CENTCOM, the U.S. military’s command for the Middle East and Central Asia, but are officially employed by the Defense Intelligence Agency.

The complaints allege that in some cases key elements of intelligence reports were removed, resulting in a document that didn’t accurately capture the analysts’ conclusions, sources familiar with the protest said. But the complaint also goes beyond alleged altering of reports and accuses some senior leaders at CENTCOM of creating an unprofessional work environment. One person who knows the contents of the written complaint sent to the inspector general said it used the word “Stalinist” to describe the tone set by officials overseeing CENTCOM’s analysis.

Many described a climate in which analysts felt they could not give a candid assessment of the situation in Iraq and Syria. Some felt it was a product of commanders protecting their career advancement by putting the best spin on the war.

Some reports crafted by the analysts that were too negative in their assessment of the war were sent back down the chain of the command or not shared up the chain, several analysts said. Still others, feeling the climate around them, self-censored so their reports affirmed already-held beliefs.

The importance of these allegations cannot really under downplayed and shouldn’t be dismissed or otherwise swept under the rug. From the President on down through the ranks of the military, and including the Members of Congress who deal with national security, military matters, and foreign policy, the number of people who depend upon accurate intelligence and honest assessments of that intelligence are probably too numerous to county. Since the vast majority of these people aren’t intelligence professionals themselves, and obviously don’t have the time to individually examine raw intelligence and analyze it in ways that would be helpful to decision making, they largely depend on the people who are interpreting the raw data, explaining what it means when viewed in context of other data, and generally providing their superiors with the information they need to make decisions. If the intelligence itself is incomplete, then the analysis is obviously going to be incomplete and the decisions that are being made are going to risk being faulty. If the intelligence is largely complete, or at least as complete as it can be, but the analysis is flawed for one reason or another then you’re going to have similar problems. Both of these issues have played a role throughout American history, including during the Vietnam War, in the years leading up to the September 11th attacks, and most prominently in the context of the Iraq War, all of which demonstrates that these are the kind of failures or mistakes that can end up costing lives and influencing events in ways that can change the course of history.

What’s particularly concerning about these reports, of course, is the idea that intelligence analysis was being changed to fit a narrative, or to avoid providing higher-ups with information that went against pre-existing narratives. At this point, we don’t know why this was happening. Was it because Defense Department civilians were pressuring the intelligence community to tone down assessments that current policy was not going to be sufficient to deal with the ISIS be? Were people in the Administration the ones putting pressure on the White House on the DoD to “get in line” with Administration policy because of general unwillingness to make the political case for wider military involvement? Were senior intelligence officials simply not willing to tell their superiors something that conflicted with what was being something, or tell them things that they clearly didn’t want to hear? Was this all part of turf battles inside the intelligence community that played a huge role in the failure to properly assess and share intelligence prior to the September 11th attacks that hasn’t really been fixed? Or is something else involved?

At this point it seems far to early to jump to conclusions regarding any of these questions, but they must obviously be answered. Intelligence, and it’s proper assessment, is essential to proper decision making and the possibility that the books are being cooked, regardless of the reason, is a serious one that could have critical implications for years to come. The only other question to ask is why it’s taken this long for these reports, which seem to be based in actions that go back as far as the summer of 2014, are only now coming to light.