BAGHDAD, Iraq—The general commanding coalition forces in Iraq predicts it will take two years of hard work to clear the so-called Islamic State from its twin capitals of Mosul and Raqqa, and then to burn out the remnants that will likely flee to the vast empty desert between Syria and Iraq.

In a Christmas Day sit-down with The Daily Beast at his headquarters, Lt. Gen. Stephen Townsend would not put specific timelines on the battle. But he mapped out a grinding campaign that he thinks is going slowly but as well as can be expected, considering how much time ISIS had to prepare and how brutal its fighters are willing to be.

“A fighter walking out of a building will hold a child over his head so we can see him through ISR until he reaches another building,” he said, using the military acronym for intelligence, surveillance, and reconnaissance.

The grim battle against ISIS is taking place against a backdrop of continuing sectarian tension in Iraq, which could get worse if newly empowered militia groups let their influence go to their heads. A new Iraqi law that goes into force this week makes militia forces here legal. Such groups—especially Iranian backed Shiite armed forces—have been accused of war crimes against Iraq’s Sunni minority. The U.S. has ordinarily eyed these units warily.

But Townsend, in an unusual statement for an American commander, said these militias been been “remarkably disciplined” allies since he arrived. That assessment marks a stark contrast with his previous tours, when deadly Iranian-manufactured bombs almost hit his vehicle, and took the lives of many of his troops.

The coalition footprint is much smaller than the 100,000-plus of Townsend’s previous tours in Iraq—somewhere south of 10,000 when troops on short term duty are added to the count. At the headquarters compound, soldiers were taking a brief break from work on Christmas to stage a spoon relay race in a hallway. One soldier dressed as Santa cheered competitors to the finish line, while those watching swigged nonalcoholic cider for some semblance of Christmas cheer.

The headquarters is tucked inside the sprawling “Green Zone” which the U.S. used to run, now turned over to Iraqi control. The Americans feel very much like visitors. U.S. authority extends to the gate of the compound—all outside is done with Iraqi government permission. Townsend’s team is very aware they are there to help, not to lead.

The Baghdad team, together with the northern based task force of special operations and conventional forces, feed a steady stream of intelligence from overhead drones to Iraqi forces on the ground. Most advisors are at Iraqi headquarters, though special ops “trainers” have joined their Iraqi advisees on missions, and the U.S. troops are also allowed to do unilateral raids with Iraqi permission.

In the process, Townsend’s forces are exposed to sights they will never forget.

“Beheading with a knife isn’t good enough anymore,” Townsend said of ISIS’s fighters. He said they use blow torches, chainsaws, and even bulldozers to crush rows of people. The coalition tries to stop such macabre displays by striking targets nearby, but that seldom helps.

A key challenge is to assist without causing insult. Sometimes, that means getting stuck between being honest with the U.S. media, while Iraqi generals are being less than forthcoming in a country where openly admitting mistakes or difficulties is not the done thing.

For instance, in the last couple of weeks, Iraqi generals told the local press that they were not pausing the Mosul assault.

But Townsend said Iraqi forces had indeed paused in their charge into Mosul over the past week or so, 60 days into their campaign, to take stock and resupply, with casualties in some units as high as 30 percent. It’s something U.S. advisors had warned them they might have to do.

“People need to rest. They need to assess how things are going because they are not going as fast as we thought,” he said.

The Iraqis are now moving in fresh reinforcements, ammunition, and taking time to repair vehicles broken in the headlong onslaught into western Mosul—all things the U.S. Army did in its 2003 charge on Baghdad when it paused on its way to taking the capital, Townsend said.

He said Iraqi generals commanding the fight met for a “lessons learned” session last week, and were forthright about what was working and what failed in battle.

The largest threat the Iraqi forces face comes from armored car bombs. Townsend showed a photo of one—a 2015 Jeep Cherokee that had been professionally armored and even fitted with a gun turret. There was even a platform on the back of the vehicle where suicide vest bombers can hang on until they reach the target.

The Iraqi army is learning to send its tanks into battle into the city—something Townsend said U.S. forces had to learn the hard way after fighting inside Iraqi urban areas.

“Quite honestly, I don’t think we trained them to do that,” he said. “They are learning to do it in combat.”

He said now the Iraqi ground forces are learning to clear houses alongside tank units, with the tank units protecting their progress from armored car bombs, or blasting holes in the side of houses so ground forces can pour in to clear them without going through booby trapped doors.

Townsend had praise for the rapid progress of the so-called Popular Mobilization Forces—mostly Shiite militias who stormed up to the outskirts of ISIS stronghold Tel Afar, west of Mosul, keeping off fighters from traveling back and forth with supplies or information.

“The PMF did advance more rapidly than we expected and they’ve done a good job,” he said.

The PMF are made up of several dozen irregular militia groups of every religious and political stripe in Iraq including Sunni and even Christian, but the majority are Shiite. Some groups formed to fight the U.S. after the 2003 invasion, and others formed after Iraq’s top Shiite cleric, Ayatollah Ali al Sistani, issued a fatwa or religious order calling on Iraqis to take up arms after ISIS seized large parts of Iraq in 2014.

Iraq’s Parliament recently passed a law making such groups legal, and placing them under the umbrella of the Iraqi armed forces, though answering directly to Iraq’s Prime Minister Haidar al Abadi.

Spokesman for the PMF Ahmad Al Asady told The Daily Beast that the law goes into force on Monday, and will help professionalize the groups. Some have been accused of committing atrocities and holding Iraqis, especially minority Sunnis, in illegal detention by the hundreds—a charge Asady denies.

He said the PMF have been holding training sessions for a year to teach their fighters how to fight according to the Geneva Conventions, including workshops with the International Committee of the Red Cross and other humanitarian agencies. The ICRC in Baghdad confirmed they’d held training sessions.

Asady said they will answer directly to the Prime Minister, though he conceded his forces get significant help including battlefield advisors from Iran.

Townsend said from what he’s seen, the disparate PMF groups are acting professionally.

“Before I got here, I read all kinds of things about the PMF, and I got here and I haven’t observed that behavior,” he said. “We’re not having allegations of bad behavior or misconduct,” and that includes absolutely no threats to U.S. personnel.

“Their internal and external comms are to keep disciplined and follow the orders of the government,” he said. “They’re saying that and that’s what we’re seeing.”

Townsend believes the new law, and the newly legalized forces, could make Iraq more secure—if they become a national guard-like force, and not a “puppet” of Iran, which he says is what Iran’s Quds Force commander Qasem Suleimani would likely prefer.

The ugly alternative would be if the PMF “becomes like the Quds Force”—Tehran’s proxy forces for its wars in Syria and Yemen—“where it is an arm of Iran, an Iraqi security force that does what Iran wants it to do,” he said.

The PMF law is only a page and a half long, and very vaguely written.

“Our government is going to try to shape it,” he said. “I hope the Iraqis choose a smart path.”

He said there are no plans to dispatch U.S. advisors to the mostly Shiite units, however.

The war is grinding on against a backdrop of continuing sectarian strife in Baghdad, and a cynicism that political change is possible.

At St. George’s Catholic Church in Baghdad, where several hundred Christians gathered to celebrate Christmas, a prominent Shiite politician spoke of unity.

“Our choice after ISIS is not civil war, is not killing each other,” said Ammar Al-Hakim, one of Iraq's most powerful Shiite politicians. “The only option we have is to live together and this requires... a national reconciliation project. We will patch our wounds together.”

But he’s attended similar church services over the years, and Iraq’s Christian community has continued to dwindle from a high of 1.5 million before the U.S.-led invasion to roughly half a million now. ISIS has only made that worse, said St. George’s Father Meyassr Behnam.

“Families are leaving, maybe 100 a month,” from Baghdad, and it’s worse in the north where Christian villages have been razed by ISIS.

Outside his church was a crèche set up in what looked like a house destroyed by ISIS, and next to it, the model of a famous church in the northern Christian city of Qaraqosh, defamed by ISIS graffiti. He pointed out that the graffiti has been artfully drawn over, changing just a few letters to transform the phrase, “Islamic State in Iraq & the Levant” to “Peace is born in Iraq & the Levant.”