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At one point, the Pentagon considered moving the operational headquarters of Africa Command, or Africom, to Djibouti. But that plan was scuttled out of concern that the government there would face too much public pressure.

Ms. Townsend said she has had her own frustrations during the Bush administration with the level of Mr. Saleh’s counterterrorism cooperation. Nonetheless, she said, “We worked out a counterterrorism arrangement that allowed us some level of activity and cooperation with Saleh’s government inside Yemen.”

“Absent Saleh, the most likely scenario is an Islamic extremist-leaning government,” Ms. Townsend said. “It becomes much less certain that we will get the kind of cooperation we get now with the Saleh government, which itself is inadequate.”

Juan Zarate, a former deputy national security adviser to Mr. Bush for counterterrorism, said he thought the Saudi government, which shares a border with Yemen, would step up its own counterterrorism operations against AQAP. Many of AQAP’s leaders were originally members of Saudi Arabia’s now-defunct al Qaeda affiliate.

“I think the most important immediate effect is that the Saudi government themselves would view themselves at risk and would devote more attention to problems along its border,” Mr. Zarate said.

Overall, the view from Washington is that the crisis in Yemen will have security implications for the United States at home and abroad.

Charles Allen, a retired veteran CIA officer and until recently the senior intelligence analyst at the Homeland Security Department, said a vacuum in Yemen’s leadership “could enhance the capabilities of al Qaeda in the Arabian Peninsula, which has already launched long-range attacks on the United States.”

“Anything that would lessen our ability to work cooperatively with the Yemeni military and its security services would be to the detriment of the United States,” Mr. Allen said.

Mr. Kirk said the Obama administration needs to prepare for the worst.

“The government in Yemen is in crisis, with armored-corps commanders flipping to the other side,” he said.

“The U.S. government should be involved to see if another government that supports our counterterrorism policy takes power. But we have to be prepared for the worst, that a government aligned with terror would take power in Sanaa.”