Yemen’s president and cabinet resigned on Thursday amid a standoff with a powerful anti-American militia, signaling deep uncertainty for U.S. counterterrorism strategy in the country and the future of a drone program in what has become a cornerstone of the global war on terror.
The resignations come a day after the Houthi militia and President Abed Rabbo Mansour Hadi signed a deal that would see the minority group withdraw from government and military infrastructure in exchange for greater political power.
After the deal was signed, however, the Houthis continued to occupy Yemen’s largest missile base in San’a and the president’s residence, while the group tried to overrun a military base and clashed with pro-government tribesmen in Marib province, which contains the country’s most significant oil infrastructure.
The Houthis represent the country’s Zaidi sect, an offshoot of Shiite Islam. They have admitted to accepting Iranian arms and training in the past, although militia leaders insist they are an organic, national force.
The group said it would prepare a reaction to the resignations on Sunday, when Parliament meets. The response hinted that the militia recognizes that it will have a hard time running Yemen unilaterally, as a minority sect with much of the country out of its control.
The U.S. finds itself in an awkward position with the Houthi takeover, as the militants have been more successful at fighting a resurgent al Qaeda force than the Yemeni national security forces, which have been trained and backed by the U.S. In recent weeks, the U.S. has tempered criticism of the Houthis.
Whether the U.S. counterterrorism strategy in Yemen can continue under the rocky political transition is unclear. Mr. Hadi personally approved a U.S. airstrike-and-drone program that targets al Qaeda leaders and training camps, with dozens of such strikes since 2009. The U.S. also trains Yemen’s elite counterterrorism units and has spent nearly $1 billion on military, economic and humanitarian assistance to the government since 2011.
U.S. officials consider Yemen-based al Qaeda in the Arabian Peninsula, or AQAP, to be the organization’s deadliest branch, the one most capable of launching global attacks. AQAP claimed responsibility for this month’s attack at Charlie Hebdo magazine in Paris that killed 12 people.
“It’s absolutely too soon to tell what impact it’s going to have on any counterterrorism partnership,” Rear Adm. John Kirby, the Pentagon press secretary, said on Thursday. “Obviously, our counterterrorism partnership and operations in Yemen have been productive and useful.…Regardless of what happens here, nothing’s going to change about our focus about going after AQAP wherever they are.”
A second Pentagon official said it is possible a Houthi-led government would welcome U.S. help against AQAP. “The Houthis are every bit as anti-AQAP as the Hadi government is,” he said.
U.S. officials said they didn’t expect Thursday’s resignations to bring an abrupt halt to American surveillance flights over Yemen used to gather intelligence on AQAP operations.
AQAP stands to benefit from the current political vacuum while the expanding Houthi force could polarize the country’s sects further, pitting the country’s majority Sunni population behind the al Qaeda militants, seen by some as the only force capable of countering the Houthis. Hard-line Sunni groups such as al Qaeda see the Zaidis as heretical. The downfall of Mr. Hadi and fellow Sunni politicians and parties could rally the sect behind AQAP.
An AQAP spokesman said in a series of text messages via secure chat that the Houthi takeover would help the group find new recruits. “It will also help us in targeting the Yemeni army and police because they will be working officially under [the] Houthis’ administration,” the spokesman said.
“It’s like the Iraqi scenario,” he added, in reference to Iraqi Sunnis’ opposition to the Shiite-led government in Baghdad, which they say discriminates against their sect.
The political marginalization of Iraq’s Sunnis and their growing opposition to the government in Baghdad has led to the resurgence of Islamic State, another extremist group and al Qaeda spinoff.
“The U.S. is trying to keep themselves open to the Houthis. The U.S. realizes, and I think the Saudis realize as well, that although the Houthis are friendly with the Iranians, they are indigenous to Yemen. And they both are desperate to maintain their influence in San’a,” said Charles Schmitz, a Yemen specialist at Towson University and scholar with the Middle East Institute.
Saudi Arabia also opposes the militia and in December cut off aid to Yemen’s government to protest the gradual Houthi takeover. Yemen relies on foreign aid to prop up the state and Riyadh has given billions of dollars in assistance to San’a since 2012.
The current crisis began in September, when the Houthis occupied the capital, forcing Mr. Hadi’s cabinet to resign in protest of the slow pace of political overhauls, including the drafting of a new constitution. Mr. Hadi took over in 2012 after the country’s two-decade autocrat, Ali Abdullah Saleh, was ousted in Yemen’s revolution.
This month, Mr. Hadi’s government stood behind a draft constitution that would divide Yemen into six federal states, which the Houthis protested, saying it would dilute the Zaidi’s political power.
Clashes also intensified Thursday in central Marib province, a stronghold of AQAP and the site of the country’s most significant oil and electricity infrastructure, including a pipeline that feeds San’a.
Houthi leader Abdel-Malek al-Houthi had demanded this week that the government step up its fight against AQAP in Marib or else his militia would storm the province. In the Wednesday deal, the government had agreed to examine the security situation there and determine a course of action.
The Houthis have quietly stationed their forces in parts of Marib, although the province is dominated by Sunnis, invoking the ire of pro-government tribes there.
Just hours after the political agreement was signed Wednesday and a cease-fire was to begin, hundreds of Houthi militants tried to storm the 7th Brigade in Marib. They were fended off by pro-government tribesmen, killing at least two and wounding six.
—Hakim Almasmari contributed to this article.