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How instability in Yemen affects the U.S.

Instability in Yemen deepened Wednesday as President Abed Rabbo Mansour Hadi fled the country in a boat to escape the Shiite Houthi rebels whose increasing power forced him from office in January.

The collapse of the government already spelled bad news for the U.S., which benefitted from the fact that Hadi allowed the American military to conduct drone strikes there against al Qaeda in the Arabian Peninsula (AQAP). With Hadi gone, the last vestiges of his power also vanish and leave an uncertain future for U.S. security.

How Yemen's crisis will impact U.S. fight against terrorism

"We have a critical counterterrorism need in Yemen," said CBS News Senior National Security Analyst Juan Zarate. "Al Qaeda branch in the Arabian peninsula, the al Qaeda brand in Yemen, is still deemed by American counterterrorism officials as being the most lethal, most active in terms of going after the West."

In addition to the top al Qaeda bomb maker, the group has dedicated senior-level al Qaeda operatives running their western operations and control more and more territory because of the chaos there.

"That's a problem because you have a safe haven with a group committed to hitting the United States that now may fall under less pressure rather than more and without a U.S. presence on the ground working with Yemeni counterparts you have less pressure," Zarate said.

The other two problems are the spread of instability across the Gulf, which makes U.S. allies in the region nervous, and the fact that there is a proxy battle between Sunni Arab allies and the Iranian-backed Houthi rebels.

Shiite rebels seize Yemen's third largest city

AQAP is also ideologically aligned with the Islamic State of Iraq and Syria (ISIS), Zarate said, but strategically they are in still in competition for who will lead the global jihadi movement. In Yemen, they could end up competing for territory, movement, operatives and resources, which could benefit the U.S., but there is also a clear risk of them forming an alliance.

"We've to make sure that we at least keep an eye on and a picture on what's happening in Yemen in particular with Western plotting. That takes deep intelligence work, that takes reliance on our allies in the region to get into these areas that al Qaeda is using to plot and to plan attacks and so keeping our eye on the ball is really important especially as al Qaeda and other actors shift," Zarate said.

An earlier version of this article incorrectly stated that the Houthi rebels are ideologically aligned with Al Qaeda in the Arabian Peninsula.