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.