BAGHDAD • After nearly nine years of war, the loss of more than 100,000 lives and hundreds of billions of dollars spent, the U.S. military mission in Iraq has formally ended.

But violence continues to roil the Mideast nation, and its political destiny is far from certain.

Defense Secretary Leon Panetta and other top U.S. officials conducted a low-key ceremony on a military base at the Baghdad airport Thursday, furling the flag to signal the official conclusion of one of most divisive wars in American history.

Panetta did not address the controversial origins of the war or Iraq's continuing troubles. Instead, he paid tribute to the sacrifices of U.S. troops, nearly 4,500 of whom were killed and 32,200 wounded since then-President George W. Bush ordered the March 2003 invasion that toppled Saddam Hussein.

"To be sure, the cost was high — in blood and treasure for the United States and for the Iraqi people," Panetta told about 200 troops and a few Iraqi officials during a 45-minute ceremony. "But those lives were not lost in vain — they gave birth to an independent, free and sovereign Iraq."

Only two U.S. bases and around 4,000 troops remained in Iraq as of Thursday, the rear guard of a force that was more than 170,000 strong at the height of the war and once controlled hundreds of bases. The last of them will depart Iraq by the weekend, officials said.

About 200 U.S. military personnel will stay in Baghdad to administer arms sales and other limited military exchanges as members of the U.S. diplomatic mission.

After more than eight years of security efforts, employees of the U.S. Embassy in Baghdad say they still find it too dangerous to work in the country outside the campus-like "Green Zone," hidden behind a series of towering walls.

But there is no sanctuary from the sectarian divisions that remain a source of violence and instability.

The Shiite Muslim-dominated government of Prime Minister Nouri al-Maliki is riddled with corruption, divided and often dysfunctional. Resentment over their political marginalization continues to simmer among the Sunni minority that ran Iraq during Hussein's days.

Some Sunnis are urging secession, or at least a state-within-a-state similar to the Kurdish-controlled zone in northern Iraq.

The government also faces continuing problems with private Shiite militias, some with close ties to Iran. Muqtada al-Sadr, the virulently anti-American cleric whose militiamen have fought and killed U.S. troops, controls the Promised Day Brigade in open defiance of the new constitution. Al-Sadr's party holds 40 seats in parliament.

The Sadrists "threaten the use of that militia if they don't get their way," Maj. Gen. Jeffrey Buchanan, chief spokesman for the U.S. military in Iraq, said. "It's an affront to Iraq's sovereignty. And potentially what you have is a government within a government."

The violence also goes on. By some estimates, an average of 30 bombings and other attacks happen each week, and about 10 deaths a day. That death toll is roughly 20 percent of the daily toll during the worst days of sectarian warfare in 2006.

More than 100,000 Iraqi civilians have been killed, according to Iraq Body Count, a website tracking the war. About 12 percent died at the hands of American forces, and the rest in terrorist attacks, sectarian violence and extra-judicial executions.

The security of civilians is now the responsibility of Iraqi soldiers and police, now visible on virtually every major street in Baghdad, searching passing cars and patrolling avenues. More than a year ago, they took over security responsibilities after U.S. forces withdrew from Iraq's cities.

With Americans gone, it is up to men like Cpl. Hatim Abdul Kareem to help control the country's endemic violence. He has his doubts. A Shiite Muslim, he lost a cousin to a sectarian killing. He fears more bloodletting after U.S. troops leave.

"After the Americans are gone, there will be war in the streets," he said. "This is not just me saying this. Other soldiers are saying this. My family, my friends — they're all saying the violence will get worse."

For the administration, the departure fulfills President Barack Obama's pledge to end U.S. military involvement in Iraq, a move polls suggest is supported by many Americans. As a candidate, Obama once called the Iraq conflict a "dumb war." But the continuing violence and fears that Iran is usurping American influence in post-war Iraq — a scenario that critics forecast before Bush launched the invasion — has made the administration sensitive to political claims that it has "lost" Iraq.

As a result, the administration made great efforts to keep a significant troop presence in Iraq, conceding to the inevitability of full withdrawal only after the Iraqis refused to grant U.S. troops legal immunity to prosecution.

Even so, U.S. involvement in Iraq is not over. Earlier this week, al-Maliki met with Obama in Washington, where they pledged to proceed with a new — vaguely defined — "equal partnership" between the two nations.

Iraq has requested more U.S. military training, the details of which will be negotiated next year.

"We need to stop thinking about Dec. 31 as the end," said Colin H. Kahl, deputy assistant secretary of defense for the Middle East. "It's not the end. It's the beginning of a new, more balanced relationship with Iraq."