DEBORAH AMOS, host:

It's been more than two months since the United States began pushing more troops into Baghdad as part of the new security crackdown. Initially, both Sunni insurgents and the Shia militia forces in Iraq's capital refrained from confronting American troops directly.

The U.S. military working with Iraqi army units established many new outposts across the city. But the sectarian struggle for Baghdad has continued. Now American soldiers often find themselves the targets of both sides, especially the Shiite militias. And sometimes fighting the very government they're in Iraq to defend.

NPR's Mike Shuster reports from the contested neighborhoods in southern Baghdad.

MIKE SHUSTER: Several hundred U.S. combat troops have taken over and abandoned Judo Academy in the Amil neighborhood of southwest Baghdad. They sleep on cots in the gymnasium, eat food trucked in from a nearby U.S. base, bathe in cold water, and on most days fight the militiamen of the Shiite Mahdi Army.

This is combat outpost attack established by soldiers of the 1st Battalion 28th Infantry. They were deployed here a month ago to stop the Shiite Mahdi Army, or Jaysh al-Mahdi, from pushing all the Sunni residents out of the area. Lieutenant Colonel Pat Frank(ph) briefed the visiting U.S. general earlier this week.

Lieutenant Colonel PAT FRANK (U.S. Army): Those areas seem to be dramatically Sunni along to the airport road. That is the extent of the cleansing that is taking place by Jaysh al-Mahdi by the time we arrived here.

SHUSTER: When thousands of additional U.S. troops began their deployment into Baghdad's troubled neighborhoods in February, the conventional wisdom had it that the Mahdi Army chose not to confront them. The Mahdi Army is led by the radical cleric Moqtada al-Sadr. And it is anti-American in the extreme. But Sadr and other militia leaders, it was said, were reluctant to challenge the American-led security crackdown.

The conventional wisdom turned out to be true in the dense Shiite neighborhood of Sadr City in northeast Baghdad, but not so true here in south Baghdad. When the Americans established combat outpost attack in mid March, they arrived in the midst of a Mahdi Army offensive against the local Sunni population.

The Americans paired with the unit of the Iraqi National Police, who told them which streets were defensible and which weren't in case of attack. It was good intelligence says Major Will Cotty when the militia hit the Americans.

Major WILL COTTY (U.S. Army): Basically, what we set up in sector and the assessment phase was over, they launched a simultaneous attack of five different outposts all on the same day.

SHUSTER: Throughout April, the militia has attacked this outpost regularly and other spots where, says Major Cotty, the company had positioned troops.

Maj. COTTY: Their main effort came the other night when they attacked our safe house on Route Menga(ph). They hit it with three RPGs, five to seven guys. They then attacked it again the next night with the same amount.

SHUSTER: The ultimate goal is to improve security for the Iraqis, especially for the few Sunni families who remained here says Brigadier General Dana Pittard.

Brigadier General DANA PITTARD (U.S. Army; Commander, Iraq Assistance Group): And the best way that you can secure neighborhoods is by living there, by being there. We're seeing more and more combat outposts and joint security stations throughout Baghdad. And what it's doing is it's getting our soldiers out with Iraqi security forces, as opposed to just being on a couple of bases and then going out.

SHUSTER: General Pittard commands the Iraqi Assistance Group. Among his many responsibilities, he is in charge of placing American trainers with Iraqi Army and police units across the country.

Unidentified Man: Sir.

General PITTARD: Are you doing all right?

Unidentified Man: I'm doing awesome, sir.

General PITTARD: Good.

Unidentified Man: (unintelligible).

General PITTARD: All right.

SHUSTER: A mile southeast of combat outpost attack is the Doura neighborhood in south Baghdad, in the past, a Sunni insurgent stronghold. Since last year, the insurgents have hit this area continually, especially its markets - attacking Shiite civilians and Iraqi security forces, virtually paralyzing the community.

This is the main Doura police station, and American trainers are here as well. They met with General Pittard along with the Iraqi police commander General Gazwan Arawi(ph), who acknowledged how difficult it's been to gain control of the area.

General GASWAN ARAWI (Iraqi Police Commander): (Through translation) Actually, it's yes. It's a lot worse, but it's more clear than before. Right now, I think, it's their last phases in their attacks here.

SHUSTER: After a little prodding, Gen. Gaswan concedes the scope of the problem he's facing. Of his 2,000-strong police force, he's lost 67 killed, nearly 400 wounded. He can put only a thousand police on the streets.

Gen. ARAWI: (Through translation) I need 3,000 active on ground. Actively, I have only 1,000, so it makes it three times what we have right now.

SHUSTER: The Shiite militias have been active in this area as well, at times with the complicity of the police who work for the ministry of the interior, which is controlled by members of the Shiite-led government. This is another murky problem for U.S. forces stationed in southern Baghdad, fighting gunmen who may in fact have the support of key figures in the Iraqi government.

Colonel Douglas Medcalf commands the team of American trainers working with Gen. Gaswan here at the Doura main police station.

Colonel DOUGLAS MEDCALF (U.S. Army): There has been some issues with the reputation of the national police, stemming from when they formed, a perception that perhaps they were militia-influenced. And as we try to overcome that stigma, the population knows that they're with coalition forces, they're legitimate. That is not a rogue group of people or impersonators that are in trying to terrorize the neighborhood.

SHUSTER: A heavily armored U.S. convoy lumbers slowly through the streets of south Baghdad. The damage is obvious as is the fear instilled in those who still live here. There's rubble and garbage everywhere, concrete blast wall separates street from street, hundreds of shops and stalls in the Doura market are shuttered, razor wire is strewn everywhere, the buildings and streets are scorched from multiple bombings.

Twenty police checkpoints in the neighborhood have slowed traffic to a trickle as the U.S. convoy passes, Iraqis stare blankly through their automobile windows. Back at combat outpost attack, Major Alex Stevenson says the presence of the police in his neighborhood isn't always a positive force either.

Major ALEX STEVENSON (U.S. Army): (Unintelligible) issues, with the Colonel Yusef, the battalion commander. I suppose it's in the works that he'll be changed out; it's trickled down back once we switch him out. It's kind of really come along; we can do a lot of positive stuff within that area.

SHUSTER: The Americans here have also lost an ally mysteriously. The previous Iraqi police commander here, a Sunni, was arrested not long ago. He was removed by someone, an Iraqi in the ministry of the interior, and is now in jail. General Pittard suspects he proves too effective at fighting the Mahdi army.

Gen. PITTARD: If you're fighting in Sunnis, no one seems to have a problem with it here. But if you're fighting against Jaysh al-Mahdi or Shia militias, it is looked on differently. That whole way of thinking has got to change.

SHUSTER: General Pittard believes combat outpost attack and others like it have initiated the process of taking back the neighborhoods of south Baghdad from armed groups on both sides of Iraq's sectarian divide.

Gen. PITTARD: By putting combat outpost attack where it's at, it has now gotten in the way of Jaysh al-Mahdi's plans to move the last Sunni enclaves out of that neighborhood.

SHUSTER: It's not yet evident whether Iraqis who still live in the streets, or who used to, see the same progress.

Mike Shuster, NPR News, Baghdad.

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