The attack on the embassy in Yemen is only part of the story in the Middle East Thursday.
Protests against have broken out across the region. They might have started as an expression of outrage over a crude online video believed to mock the Prophet Mohammed. But it's not clear where things go from here.
The unrest is already proving to be a difficult challenge for the Obama administration, which has been holding out hope for positive change in a volatile region.
Alan Baker, a former Israeli Ambassador to Canada, said all that's happening should be "a clear wake up call" to Washington.
Baker is based at a think tank called the Jerusalem Center for Public Affairs. Baker said the US needs to stop thinking about the turmoil in region as an "Arab Spring".
"The US administration has to remove the sunglasses and look clearly at what's happening in the Arab world," he said. "And it's not a spring. And it's brought with it a huge amount of threats and problems."
The situation in Egypt might present the biggest problem for Washington. Violent clashes broke out Thursday near the US Embassy in Cairo. It wasn't clear whether demonstrators were protesting the film that mocked the Prophet Mohammed. Or, if they just showed up to settle old scores with Egyptian security forces.
A full day after protesters climbed the wall of the embassy, pulled down the American flag and hoisted a black banner like the one used by al-Qaeda groups, President Mohammed Mursi weighed in on events for the first time. He issued a recorded statement broadcast on Egyptian TV, condemning the killing of US Ambassador Christopher Stephens in Benghazi.
"These kinds of acts jeopardize the relationships between people in the world. We are not in any way, we are not accepting those acts. We are against those acts. They are not with the people will. They are against the free-willed people in the whole world," President Mursi said.
Mursi went on to condemn the anti-Muslim video. He said Egyptians have a right to protest. But added that his government is keen to prevent more attacks on US diplomatic facilities. Mursi mentioned that he spoke with President Obama on the phone.
What's not clear is how satisfied the White House is with Mursi's response to the crisis.
Obama did an interview Wednesday with the Spanish TV network Telemundo. And in an excerpt aired on MSNBC, the president was asked if he considers Egypt's current regime an ally of the United States. Here's what followed:
"You know, I don't think we would consider them an ally, but we don't consider them an enemy. They are a new government that is trying to find its way. They were democratically elected," President Obama said.
Obama said Egypt's new government is a work in progress. And in regards to the current situation, the president said Egypt needs to take its responsibility to protect the US Embassy and personnel seriously. Or that's going to be a big problem.
"President Obama is starting to play hardball," said Shadi Hamid, an Egypt expert at the Brookings Institution.
"I think he does want to sent a message that US support cannot be taken for granted. We're willing to help you with your economic recovery. But we expect certain things in return, especially when it comes to fundamental issues of national security," Hamid said.
Hamid said no one should be surprised that Islamist groups such as Egypt's Muslim Brotherhood have made great political strides during this period of turmoil in the region. But Washington should not give up on the Arab Spring.
"What the Arab Spring provides for the US is a second chance," he said. "I think that we got things wrong for five decades. We were supporting dictatorships and doing so against our ideals. And that's one of the reasons why Arabs dislike or hate the US. It doesn't come from nothing."
Hamid said one reason Washington needs to engage with the Arab world's new political players that the alternatives are worse.
To the right of the Muslim Brotherhood, for example, are the ultra-conservative Salafi Muslim groups. The same ones suspected of killing Ambassador Stevens. And raising the black flag at the US Embassy in Cairo.