The intimidating myth of an all-powerful military in Pakistan has been smashed in public view.

The first cracks began to appear two years ago, when thousands of Pakistanis rallied alongside an ousted prime minister who had railed against the generals’ iron grip on politics. A year later, angry mobs stormed military installations and set them aflame.

Now comes another searing rebuke: Voters turned out in droves this month for candidates aligned with the expelled leader, Imran Khan, despite a military crackdown on his party. His supporters then returned to the streets to accuse the military of rigging the results to deny Mr. Khan’s allies a majority and allow the generals’ favored party to form a government.

The political jockeying and unrest have left Pakistan, already reeling from an economic crisis, in a turbulent muddle. But one thing is clear: The military — long respected and feared as the ultimate authority in this nuclear-armed country of 240 million people — is facing a crisis.

Its rumblings can be heard in once unthinkable ways, out in the open, among a public that long spoke of the military establishment only in coded language.

“Generals should stay out of politics,” said Tufail Baloch, 33, a protester in Quetta, a provincial capital in the country’s restive southwest.

“The military should focus on combating terrorism, not managing the elections,” said Saqib Burni, 33, who demonstrated in Karachi, the country’s most cosmopolitan city.

No one thinks that the military, with its lucrative business interests and self-image as the backbone holding together a beleaguered democracy, will cede power anytime soon. And even after this election, in which Mr. Khan’s allies won the most seats, the generals’ preferred candidate from another party will become prime minister.

But after the outpouring of voter support for Mr. Khan — and the botched effort at paralyzing his party — an overwhelming swell of Pakistanis now view the military as yet another source of instability, analysts say.

As the military’s legitimacy is tested, the country is waiting to see how the army’s chief, Gen. Syed Asim Munir, will respond.

“This is the biggest institutional crisis that the military has ever faced in Pakistan,” said Adil Najam, a professor of international affairs at Boston University. “It is not just that their strategy failed. It’s that the ability of the military to define Pakistan’s politics is now in question.”

Since Pakistan’s founding 76 years ago, the generals have either ruled directly or been the invisible hand guiding politics, driven by a view that politicians are fickle, corrupt and insufficiently attuned to existential threats from archrival India and the wars in Afghanistan.

But after a mounting public outcry forced the country’s last military ruler, Gen. Pervez Musharraf, to resign in 2008, the military’s power calculus changed. While true democracy had proved unstable, ruling the country directly opened the military up to too much public scrutiny. Allowing civilians to be elected in democratic votes — while still steering the policies that mattered — could insulate the military from public criticism, or so the thinking went among top brass.

The result was a veneer of democracy that had all the trappings of participatory politics — elections, a functioning Parliament, political parties — but none of the heft. For a decade, prime ministers came and went, ushered in when the military favored them and forced out when they stepped out of line.

The fallout from the ouster in 2022 of Mr. Khan, a populist leader who pitched himself as an alternative to the country’s entrenched political dynasties, torpedoed that uneasy status quo. Once a darling of the military, Mr. Khan blamed the generals for his removal, popularizing once unimaginable rhetoric among the country’s huge population of young people that the military was a malevolent force in politics.

“There is a new generation that doesn’t see the military as something that rescues them from bad politicians — it is seen as an institution which is in fact part of the trouble,” said Ayesha Siddiqa, author of “Military Inc.: Inside Pakistan’s Military Economy.”

The military’s response to Mr. Khan’s resurgent public support was bungled at best — and severely miscalculated at worst, analysts say.

The state censorship machine could not keep up with the flood of viral videos on social media spreading Mr. Khan’s anti-military messages. Arrests and intimidation of military veterans and those in the country’s elite who backed Mr. Khan only seemed to isolate the military from one of its key support bases and drive voters to cast ballots just to spite the generals.

As Mr. Khan was slapped with multiple lengthy prison sentences days before the vote, it deepened people’s sympathy for him, instead of demoralizing them and keeping them home on Election Day, analysts and voters said.

The military’s strategies “completely backfired,” said Aqil Shah, a visiting professor at Georgetown University and author of “The Army and Democracy: Military Politics in Pakistan.” “They miscalculated the amount of resentment and backlash against what the military was doing and the other parties that were seen as being in collusion with it.”

In the days after the election, the military’s favored party of the moment, led by former Prime Minister Nawaz Sharif, announced that it had cobbled together a coalition with the country’s third-largest party and others to lead the next government.

But as candidates aligned with Mr. Khan won the most seats, it proved to Pakistanis that there are limits to the military’s power to engineer political outcomes. And any social legitimacy that the military had left, analysts say, was eroded by widespread allegations of vote tampering to narrow the winning margins among Mr. Khan’s allies.

For now, most expect the generals to stay the course and back the government led by Mr. Sharif’s party, hoping the uproar subsides. But in the months and years to come, they will need to rebuild public trust to stabilize the country, and they have few good options.

Should the current unrest boil over, analysts say, the military may use an even heavier hand to reassert its authority, like imposing martial law. But when the generals have exerted their authority forcibly in the past, they have tended to do so with the public’s support at times of growing exasperation with elected governments.

General Munir or his successor could strike a deal with Mr. Khan to bring him back into politics in the hope that it quells the unrest. While many in the military’s top ranks view Mr. Khan as self-involved and an unreliable partner, his cultlike following could be used to change public opinion about the military.

Though Mr. Khan has portrayed himself as a martyr for democracy, most analysts believe that he would embrace the military and its role in politics again if he was allowed to return to the political scene. But, so far, General Munir has appeared to be steadfast about keeping Mr. Khan out of politics.

The only certainty, experts agree, is that the military’s prominent role in politics is here to stay — as is the instability that the country has been unable to shake.

“What’s unfolding in front of us is something that will lead to a new model of the military’s relationship with politics and society,” Mr. Najam, the professor at Boston University, said. “We don’t know what that will be. But what we know is that the military will remain a force in politics.”