ISTANBUL — The almost ungovernable Yemen became a country without a government Thursday when President Abdu Rabu Mansour Hadi, his prime minister, and Cabinet resigned en masse just hours after concluding a tentative peace deal with Shiite Houthi rebels, who are seeking greater autonomy for their northern province.

The straw that broke the camel’s back was the rebels’ failure to hand over one of the president’s senior aides, who had been snatched over the weekend and whose release was a key provision in the deal. The collective resignation came after days of turmoil in the Yemeni capital, Sana’a, where rebels stormed the presidential palace and then bombarded and surrounded the house Hadi had taken refuge in.

Shiite rebels loyal to Abdulmalik al-Houthi were meant to have withdrawn their forces from the capital, most of which they seized last September, but decided to keep some of their troops stationed in Sana’a on the grounds that they couldn’t trust Hadi to fulfill his side of the bargain struck Thursday, including amending a draft constitution they opposed.

The stage now seems set for the outbreak of full-fledged sectarian civil war, one that al Qaeda in the Arabian Peninsula, the terror network’s most dangerous and capable affiliate, is likely to exploit for its advantage.

Hadi’s unexpected resignation sent much of Washington scurrying to figure what it could mean for the ongoing war against AQAP. The intelligence sharing between the two nations and the United States’ ability to conduct drone strikes with impunity, even after civilian deaths, made Yemen a keystone to the U.S. war against AQAP. Given that the Houthis so far not have officially taken charge, making it unclear who will lead the country, Pentagon and intelligence officials could not say how they would have to readjust—only that they would have to.

“The relationship [with Yemen] will have to be revisited given these developments,” a senior defense official told The Daily Beast.

On Thursday, just hours before the Hadi government collapsed, House Armed Services Committee Chairman Mac Thornberry told The Daily Beast that the uncertainty in Yemen would undoubtedly affect the U.S. campaign against AQAP there.

“I’m worried this could be like Syria,” where there is limited ground intelligence, Thornberry said. “You can only do so much with overhead surveillance” and without on-the-ground sources.

Last year, President Obama cited Yemen as a model, claiming that a year of a relentless drone strikes aimed at degrading the top and middle ranks of AQAP was working. That boast was never supported by the facts on the ground: AQAP expanded its grip in the south, and some of the Yemeni government’s assistance to the United States often had the appearance of double-dealing under the rule of Hadi’s predecessor, Ali Abdullah Saleh.

The Obama claim also looked threadbare in the wake of last week’s terror attack in Paris on the French satirical newspaper Charlie Hebdo, which AQAP claimed responsibility for, insisting it had directed and funded the operation.

Even so, the Yemeni government has been useful for Washington in the fight against al Qaeda, and a Yemen embroiled in a likely civil war between the country’s Sunni majority and minority Shia, who have long resented their marginalization from government power, can only spell more trouble.

The deal struck Thursday with the rebels looked highly improbable, even before the ink was dry. The country’s prime minister, Khaled Bahah, and Cabinet resigned ahead of the president. In a letter to Hadi, Bahah said he and his government colleagues wanted nothing to do to with the “destructive political chaos.” “[We resigned] so that we are not made party to what is going on and what will happen,” he wrote.

Yemeni Information Minister Nadia al-Sakkaf earlier had posted on Twitter that she couldn’t see why the deal would hold when the rebels had secured what they wanted—more power.

Even before the resignation of the government the sectarian power struggle was playing havoc with the government’s battle against AQAP. On Tuesday, as the presidential palace was being stormed, al Qaeda fighters came close to assassinating a top army commander in the south, killing five of his guards in the attack, military officials said.

Iran, which has been accused of backing and helping to train the Houthis, is likely to benefit from the rebels consolidating their hold on the capital. Rebel control of the shoreline opposite Saudi Arabia’s Ras Isa marine terminal already was worrying Riyadh.

“Regional actors Iran and Saudi Arabia are inflaming the situation as each seeks to block the influence of the other,” researchers at the Soufan Group, a New York-based risk consultancy firm, warned midweek in an intelligence brief.

“While the causes of Yemen’s crisis are intensely local—having to do with longstanding issues of corruption, tribal and North-South differences, and a constitution in need of amending—it is being amplified both by meddling regional actors and a menacing terrorist group with international reach,” the researchers noted.

Saudi Arabia convened a meeting of Gulf countries on Wednesday, threatening unspecified measures to “protect their interests” in Yemen. Saudi influence has waned in the country with the rise of AQAP there and the strengthening of Iran-backed Shiites, and Riyadh is likely to focus on completing new frontier defenses to seal as best it can the mountainous border. It earlier cut financial aid to its neighbor, an economic lifeline for the Arab world’s most impoverished nation.

The public humiliation of the country’s Sunni government had already triggered the anger of Sunni Muslim tribes in the south, who closed briefly the port of Aden and have threatened to turn off the oil pumps. The prospect now is that the country will fragment.