The troops have come home, the flag has been been lowered, and the Iraq War is officially in the past for the U.S. military. But the military is holding on to a major souvenir of the war: a massive database packed with retinal scans, thumb prints and other biometric data identifying millions of Iraqis. It will be a tool for counterterrorism long after the Iraq War becomes a fading memory.

U.S. Central Command, the military command responsible for troops in the Mideast and South Asia, confirms to Danger Room that the biometrics database, compiled by U.S. troops over the course of years, will remain U.S. property. “Centcom has the database,” says the command’s chief spokesman, Army Maj. T.G. Taylor, who says it contains files on three million Iraqis. The U.S.-sponsored Iraqi government, in other words, doesn’t control a host of incredibly specific information on its citizens.

For much of the war, U.S. troops carrying viewfinder-like scanning devices kept digital records of the Iraqis they encountered. Some Iraqis got their unique identifiers recorded because they were suspected insurgents on their way to detention centers. Residents of violent cities like Fallujah would only get to return home from travel if they showed U.S. troops an ID card complete with biometric data. Iraqis underwent iris scans when they wanted to join the police. So did Iraqis who worked on U.S. bases.

It was all part of an effort to answer the war’s most vexing challenge: distinguishing insurgents from Iraqi civilians. And that effort isn’t going away, even after the war technically ended. It’ll be part of U.S. counterterrorism missions for a long time to come.

“Certainly, if someone was in another country or another place and showed up somewhere, we’d compare information to see if it’s someone we had info on,” Taylor explains. For instance, “if they show up in Afghanistan, we collect biometric data [on the individual, maybe] we don’t see them there. But we run it through this database and we see them show up.”

The digital database is the property of Central Command’s intelligence shop in Tampa, Florida. It is conspicuously not in the control of the Iraqi government. Taylor says that the Iraqis might be able to access the database’s contents if they go “through the [U.S.] embassy” in Baghdad.

“Common sense-wise, we still have an interest there in helping our Iraqi partners,” Taylor explains, “and that information might be helpful to them should there be any issues.”

Taylor doesn’t say why the U.S. didn’t hand over its biometrics toy to the Iraqis. But there’s an obvious reason: Iraq’s sectarian divides have not healed. And a database filled with uber-specific information about approximately 10 percent of Iraq’s population could represent a wish list for a death squad, militia or insurgent group — some of which are aligned with Iraqi political parties.

It’s not an idle fear. The day after the U.S. departed, a court beholden to Iraq’s (Shiite) prime minister issued an arrest warrant for the (Sunni) vice president on terrorism charges. “Three of my brothers have been killed because of my participation in building a new Iraq, regardless of all I have done,” the incredulous VP, Tarek al-Hashemi, told Eli Lake of Newsweek. Hashemi, who is Iraq’s highest ranking Sunni, blamed the U.S. for leaving Iraq in Maliki’s hands.

Iraqis aren’t the only ones to wind up in huge U.S. biometrics databases. Afghans, too, have been scanned by the millions. As far back as 2005, detainee biometric data from both Iraqis and Afghans turned up in an obscure Pentagon anti-terrorism database called the Department of Defense DNA Registry. Documents released by WikiLeaks suggest that the U.S. even seeks to collect bio-data on foreign leaders.

Now that Central Command is keeping the Iraqi database, it’s clear that the military isn’t going to get rid of its troves of super-specific data once the wars end. Nor will it trust its nominal local allies to maintain them. (Some in the military have complained to Danger Room in the past that the Iraqi soldiers and cops they train aren’t great at taking eye scans and thumb prints from detainees.) It’s an intelligence tool, Taylor says, not a broad targeting list.

“We have this information, and rather than cull through it all and say ‘bad guy, good guy, bad guy, good guy, it’s better to just keep it, because that would be very time consuming,” Taylor says. “Biometric data was collected on people who worked on the bases. You’re a good guy; you worked here. It’s not like we’re collecting [data] on an enemy.”

Photo: U.S. Air Force