The president of Yemen has resigned after months of pressure from rebels. Here's what led to it, and why you should care. (Gillian Brockell/The Washington Post)

The Obama administration has been forced to suspend certain counterterrorism operations with Yemen in the aftermath of the collapse of its government, according to U.S. officials, a move that eases pressure on al-Qaeda’s most dangerous franchise.

Armed drones operated by the CIA and the U.S. Joint Special Operations Command remain deployed for now over southern Yemen, where al-Qaeda in the Arabian Peninsula is based. But some U.S. officials said that the Yemeni security services that provided much of the intelligence that sustained that U.S. air campaign are now controlled by Shiite rebels, known as Houthis, who have seized control of much of the capital.

Even before the disintegration of the government, officials say, the growing chaos in Yemen had resulted in a steady erosion
in intelligence-gathering efforts against AQAP and a de facto suspension in raids by Yemeni units trained, equipped and often flown to targeted al-Qaeda compounds by U.S. forces.

“The agencies we worked with . . . are really under the thumb of the Houthis. Our ability to work with them is not there,” said a senior U.S. official closely involved in monitoring the situation. In a measure of U.S. concern over the crisis, officials also signaled for the first time a willingness to open talks with Houthi leaders, despite their suspected ties to Iran and antipathy toward the United States.

The developments have unraveled a campaign that President Obama described last year as a model for how the United States should fight terrorist groups, and avoid being drawn more directly into overseas conflicts. The turmoil in Yemen has exposed the risks of that strategy, with U.S. officials now voicing concern that the suspension in operations in Yemen could enable AQAP — which has launched a series of plots against the United States and claimed credit for the attacks in Paris this month — to regroup.

“The chaos has aided al-Qaeda,” said the senior U.S. official, who like others spoke on the condition of anonymity because of the sensitivity of the matter. “There’s no question in our mind that al-Qaeda has gotten a breather.”

The White House disputed that joint efforts against al-Qaeda had halted. White House spokesman Alistair Baskey said that “the political instability in Yemen has not forced us to suspend counterterrorism operations” and that “we also continue to partner with Yemeni security forces in this effort.”

Asked if those forces were still intact and functional, a senior administration official said, “It is difficult for me to assess what is a very fluid situation on the ground.”

Other U.S. officials said that joint operations had been deteriorating since last fall, when Houthi militias began a series of advances toward the capital of Sanaa, but that cooperation had broken down in recent days amid a Houthi assault that culminated with the resignation of Yemeni President Abed Rabbo Mansour Hadi, a staunch U.S. ally.

Before that development, U.S. military trainers and advisers had continued working closely with Yemeni counterterrorism forces, primarily from al-Anad air base, a Yemeni military installation in the southern part of the country.

A senior military official said that counterterrorism training with Yemeni units has been put “on hold,” but that partnered operations between U.S. and Yemeni forces are still ongoing in areas outside the capital.

The Pentagon has been tight-lipped about how many U.S. troops it has deployed to Yemen, but the senior U.S. official said the total number of trainers and advisers numbered in the “dozens” and that the presence had gradually increased over the past two years. The U.S. advisers could accompany Yemeni units on missions around the country, and even provided helicopter transport during operations, but were precluded from directly engaging in combat.

The tangled international relations in Yemen

U.S. officials and analysts have said the most reliable Yemeni units were assigned to the Interior Ministry. Their training and equipment, officials said, were designed exclusively for counterterrorism missions, meaning that they were not capable of fending off the Houthi advances and were never summoned to Sanaa to protect Hadi.

U.S. advisers also spent years training units from the Defense Ministry that until 2012 had served under the command of one of the sons of then-President Ali Abdullah Saleh, the long-standing leader of Yemen who was forced from office three years ago but is suspected of having colluded with Houthi elements in recent months to oust Hadi.

Some of the U.S.-trained Yemeni troops resisted the Houthis’ advance into Sanaa, but others stepped aside or may even have cooperated with the rebels, the senior U.S. official said. The senior U.S. official said that the United States “wouldn’t be averse” to talks with the Houthis on subjects including permission to continue operations against AQAP. “We’re not against the Houthi movement.”

Yemeni military leadership ranks were overhauled in 2012 largely to remove Saleh relatives and loyalists. April Longley Alley, a senior analyst and Yemen expert with International Crisis Group, described the outcome of that effort as “an absolute disaster.”

“Some of the moves were good, but collectively they were very damaging,” Alley said. “In the transition, some of the elite troops lost privileges. This created angst towards Hadi and the transition. Some even joined the Houthi.”

As a result, Alley said, “al-Qaeda is gaining strength and the Houthis are at the forefront of fighting them, which creates its own problems and fuels recruiting for al-Qaeda.”

U.S. officials said they are weighing whether to begin withdrawing military trainers and liaison officers. There is no plan to close the U.S. Embassy, but the senior U.S. official indicated employees from the State Department, CIA and other agencies will probably be withdrawn.

“We will be bringing our numbers down,” the official said.

U.S. officials expressed hope that counterterrorism operations could resume if the political conflict in Yemen is resolved.

“It’s unclear where that is going to fall out,” said a senior administration official. “It is very hard to say until we see what emerges from the current vacuum.”

Although AQAP claimed credit for the attacks in Paris this month, U.S. officials have said they have not uncovered evidence of direct involvement by the group after one of the gunmen, Chérif Kouachi, returned to France from Yemen after getting training and as much as $20,000 from the organization.

AQAP’s plots targeting the United States include an attempt to bomb a Detroit-bound airliner on Christmas Day 2009, a plan that failed only when the bomb sewn into the operative’s underwear failed to ignite. The group has not been linked to any major attacks outside Yemen in recent years but continues to be regarded as the most immediate terrorism threat to the United States.

Michael Vickers, undersecretary of defense of intelligence, described AQAP as “the most dangerous of al-Qaeda’s organizations” in a speech in Washington this week.

The United States has sought to counter the AQAP threat through a campaign of airstrikes that began in late 2009, involving drones flown from separate bases outside Yemen operated by the U.S. military’s elite Joint Special Operations Command and the CIA.

The pace of U.S. airstrikes has tapered off, with no known attack since Dec. 6. With Hadi’s departure, the United States may no longer have explicit Yemeni permission for the drone campaign. Even if it were to continue, U.S. officials said it may become increasingly difficult to find targets.

“The issue would be whether you have the intelligence you need,” the senior U.S. official said. “To a large extent, that was a product of the cooperation we got from the Yemenis.”

Greg Jaffe contributed to this report.