NBC’s Richard Engel reports:

Flying into in Mogadishu isn’t for the faint of heart. We arrived on African Express, one of only two airlines still operating in Somalia. It’s soon clear why there are so few flights – sitting on the runway is the wreckage of a plane.

It is a fitting first impression of this country, which hasn’t had a functioning government in 19 years.

Just getting your bags is something of a free-for-all here. At baggage claim, it’s anarchy. There are no belts or X-ray machines – even Customs is nowhere to be found.

Finally, we meet our hosts: African Union peacekeepers.

There are about 5000 active peacekeepers in Somalia. Their mission is to try to prop-up the ailing Somali government. Which is so weak, it only controls a few square miles of Mogadishu. The only pocket of authority is Somalia’s version of the White House.

While US-backed President Sharif Sheikh Ahmed has the nicest house in town, he can’t go much further than his palace gardens.

President Ahmed hopes to restore security to his country and the basic framework of law and order. “What we need to do is build our institutions,” he says. “That’s our first priority.”

His problem is that most of this vast, seething city is controlled by al-Shabab – a ruthless local branch of al-Qaida.

Most people here live in fear. Even at one of Mogadishu’s only health clinics, hundreds line up for treatment, but often wait until the pain is unbearable.

Fatima brought her nine-month-old daughter Miski for treatment only after the girl’s face had become covered with painfully infected boils.

“I almost never go outside,” Fatima tells me. “I’m too frightened.”

Like most Somalis, Fatima is afraid of al-Shabab.

The militants have made Somalia their newest safe-haven. In areas under their control they have imposed an unusually strict form of Islamic law.

Women are stoned for adultery and must wear face veils, but bras are forbidden. Calling gold anti-Islamic, the militants have ripped the fillings from people’s teeth. Also banned are music, movies, and even schools bells.

There were 1.5 million people in this city a few years ago – now only 700,000 remain. Anyone who can leave has already left.

Mogadishu today is the most war-torn, dilapidated city I’ve ever seen. But what’s happening here is far worse than just these destroyed buildings. The majority of the militiamen terrorizing the city are under 16-years-old. Teenagers – empowered by chaos to enter people’s homes, lash women for dressing inappropriately and chop off the limbs of accused thieves.

Under a thorn tree I meet 20-year-old Abdel Abdi and Ismail Abdullah, 18. Both claim they were falsely accused of theft.

Their punishment was amputation of the right hand and left foot, while their parents were forced to watch.

“I tried to call out to my mother and say, please somebody save me,” Abdi says.

“One woman had a miscarriage as she watched,” says Abdullah.

The young men showed me how al-Shabab stretched their wrists and ankles before slicing them off with a butchers’ knife.

But for Abdi the punishment continued. He says militants returned 15 days later and sawed off more of his leg. Just to make him suffer.

“The leader put three fingers on me and said we have to cut off this much more,” Abdi remembers.

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The US military and intelligence services are aware of al-Qaida’s growing presence in Somalia. But there’s little desire to come here to fight.

In 1993, US troops invaded Somalia to stop clan warfare that was causing mass starvation. An American helicopter was shot down, and a soldier’s body dragged through the streets. The events were retold in the film Black Hawk Down.

Today, the US involvement is mostly from afar. Washington backs the African peacekeepers in Somalia, who in turn tiptoe around al-Shabab.

Their spokesman, Ugandan Major Barigye Ba-Hoku showed me the neighborhoods controlled by al-Shabab. But he says his troops don’t go there.

“We don’t leave the main roads too much. This is a peacekeeping mission. We try as much as possible to minimize the causalities.”

Peacekeepers say they don’t have a mandate to fight al-Shabab. Or enough troops to do it.

But now, 17 years since Black Hawk Down, the United States is secretly increasing its involvement in Somalia and gathering intelligence under the cover of darkness.

Every night here, we’ve been hearing the unmistakable sound of American drones buzzing in the sky. They seem to be flying very low and circle every 10 to 15 minutes. There are drones flying over Mogadishu on a regular basis, really on a nightly basis. I think that intelligence has its eyes peeled.

Their eyes are peeled because some of al-Shabab’s top commanders are American citizens.

A 26-year-old from Alabama named Omar Hammami has become one of al-Shabab’s leading recruiters of fellow Americans, under the name Abu Mansoor Al-Amriki.

What is happening here has direct ties to the United States. Using internet videos and rap songs, Hammami has even attracted, for the first time ever, American suicide bombers.

Seventeen peacekeepers and several civilians were killed last September when a suicide bomber attacked their headquarters. Militants identified the bomber as a Somali-American who had been living in the Twin Cities.

US counter-terrorism officials tell theGrio around 50 Americans, most of them of Somali origin, and many hailing from Minnesota, have come here to fight.

The American connection has raised flags at both the FBI and CIA.

“I think you could characterize this as Grade-A problem,” says Phil Mudd, former chief of counter-terrorism for the CIA. “The reasons are simple. The number of times you get a substantial number of American kids – I don’t care if they’re Somalis or they’re from Lincoln, Nebraska traveling overseas to train with people who are connected to al-Qaida – in these kinds of numbers, that is very rare.”

Rare, and dangerous, because al-Shabab is expected to attract more fighters – and more Americans – as its safe-haven in Somalia grows.