A mass of protesters pushing through the gates of the national army headquarters. An angry mob setting a senior military official’s residence aflame. Demonstrators looting a school run by a paramilitary force.

Once unthinkable, the scenes of violent protest that broke out across Pakistan on Tuesday after the arrest of the former prime minister, Imran Khan, seemed to cross a line against defying the army that has rarely been breached in Pakistan’s turbulent history. Since the country’s founding 75 years ago, the military has kept a steady hold on the country’s politics and foreign policy, carrying out three successful coups and ruling the country directly for several decades.

Even under civilian governments, military leaders have kept an iron — if cloaked — grip on power, ushering in politicians they favored and pushing out those who stepped out of line. Few dared any open defiance.

When politicians or other civilians complained, it was almost always in code, speaking vaguely of “the establishment” or “the sacred cow,” rather than calling out the country’s military or its powerful Inter-Services Intelligence agency explicitly. They knew what could happen if they went further: disappearances, arrests, lives in exile.

Then came Imran Khan, a former global cricket star turned populist politician and once a regular fixture in London’s fashionable crowd, who had languished on the sidelines of Pakistani politics for over two decades since retiring from the sport.

Mr. Khan rallied street power, promising to tackle the country’s deep economic troubles and end its endemic corruption, while offering an alternative to the country’s entrenched political dynasties. The military was accused at the time of paving the route to power for Mr. Khan in 2018, pressuring his opponents to withdraw or change sides and cowing the news media.

But relations soured after he was ousted as prime minister in a parliamentary no-confidence vote in April 2022, with Mr. Khan railing vehemently at the generals, accusing them of conspiring against him and his political movement.

For months, Mr. Khan had called out a senior Pakistani military intelligence general by name, accusing the commander of being behind a shooting that wounded him in November. And he had skipped court appearances for a slew of corruption cases lodged against him — almost daring the authorities to arrest him. His supporters followed suit, taking to social media to disparage the military and accuse it of subverting democracy.

By Tuesday, the authorities appeared to have had enough, and arrested Mr. Khan in a clear attempt to reassert control.

If the arrest was in many ways a return to the old order of Pakistani politics, the reaction to it was anything but. As Mr. Khan was taken away, his supporters erupted across the country in protests targeting military installations — urged on by his admonition to fight. The crowds channeled both the anger that had been brewing since Mr. Khan was ousted from office and the frustration with a severe economic crisis, in which record inflation has sent the price of basic goods soaring

Demonstrations continued in major cities Wednesday, deepening the turmoil and prompting the army to deploy units in at least two provinces. In some places, protesters fiercely fought the security forces, which lobbed tear gas canisters and brandished batons in an effort to disperse the crowds.

Many officials fear that extended protests could bring the country to a standstill, and that the government led by Prime Minister Shahbaz Sharif could struggle to rein them in. The attacks by protesters on military structures also laid bare damage to the military’s reputation that will not be easily undone.

“This has become a perfect political storm with very unpredictable consequences,” said Maleeha Lodhi, a former Pakistani ambassador to the United States and Britain. “In the past the army acted as an arbiter of political disputes. Today, the country has no institution that can play that role.”

On Wednesday, Mr. Khan appeared in a police headquarters-turned-courtroom in the capital, Islamabad, where a court had authorized the authorities to detain him for eight days in connection with a corruption case involving the transfer of real estate. Mr. Khan denied the charges and expressed concerns for his safety while in custody, local news media reported.

Separately, Mr. Khan was also charged in a different case for unlawfully selling state gifts during his tenure as prime minister.

At least five people have been killed in the protests since Tuesday, local news outlets reported, and more than 1,000 people have been arrested in Punjab Province alone. The authorities also shut off the internet in parts of the country in an attempt to quell the unrest.

But the crackdown has done little to dissuade the protesters, and the military, under a new army chief, Gen. Syed Asim Munir, is in a precarious position.

Because Mr. Khan has cultivated deep support in the military’s own ranks, escalating the crackdown could cause a rift that further destabilizes an institution already facing one of its most serious crises since 2007, when the last military leader to seize power, Gen. Pervez Musharraf, stepped down amid public outcry.

Given the strains in the military, General Munir “is possibly under pressure from the military’s networks, perhaps some senior generals, to back off, take an off-ramp and reconcile” with Mr. Khan, said Asfandyar Mir, a senior expert at the United States Institute of Peace.

A harsh crackdown on protesters also risks further eroding the military’s popular support, which had endured for decades  despite the generals’ insistence on shaping the country’s politics.

Many Pakistanis still see the army as a moderating force helping to keep corrupt political dynasties in line. Soldiers have been on the front line of relief after devastating flooding and other disasters, and in putting down terrorist campaigns by the Pakistani Taliban in 2014 and 2017.

That popularity was maintained for years after Mr. Khan’s ascent to prime minister. But when Mr. Khan was ousted from power in April by the Parliament, it was again with the perception of a military green light to remove him, after he had begun antagonizing the generals.

Mr. Khan’s criticism of the military since then has resonated even beyond his existing support base, and voters rewarded his party with significant victories in elections for vacant parliamentary seats in several provinces. Mr. Khan has also called for the government to hold an early general election.

“It’s hard to see how the situation de-escalates from here,” wrote Madiha Afzal, a fellow at the Brookings Institution in Washington, in a text message. “Khan’s popular support has protected him against the establishment’s assertiveness until now. But now that the establishment has asserted itself, it’s hard to see it backing down anytime soon.”

She added, “Volatile, dangerous times ahead for Pakistan.”

Salman Masood contributed reporting.

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