Pakistan’s latest imbroglio involving a former prime minister, Imran Khan, could end up weakening the military, the only institution that has kept a semblance of order in the nuclear-armed, geostrategically located, perennially chaotic country.

The country’s supreme court ruled on Thursday that the populist opposition leader had illegally been arrested two days earlier, and ordered his immediate release. Mr. Khan, who faces a number of corruption charges that he claims are politically motivated, must still stand trial.

A paramilitary group conducted the dramatic arrest on Tuesday. In ordering Mr. Khan’s release, the high court’s chief justice, Umar Ata Bandial, complained on Thursday that nearly a hundred troops entered the court at Islamabad to make the arrest even after Mr. Kahn had already surrendered. “What dignity remains of the court if 90 people entered its premises? How can any individual be arrested from court premises?” Mr. Bandial said.

In reality, though, the court, like pretty much every Pakistani civil institution, is far from dignified or well-respected in the country. Ousted statesmen are routinely accused, and often found guilty, of corruption and other charges that are at times tailored to fit political whims. Rather than voters, politicians often serve at the will of the army.  

Pakistan is “chaotic. It’s an absolute mess. A near failed state, and it will be a mess 50 years from now, ” a senior fellow at the Center for Security Policy, Grant Newsham, tells the Sun. “The civilian government is weak, inept, and fragile. The military is the one power that counts.” Yet, he adds, “now the military is challenged.”

When he was elected prime minister in 2018, Mr. Khan was favored by the generals. Relations soured, though, once the premier attempted to name an army chief who was answerable to him, rather than to the military establishment. In April of last year, Mr. Khan was accused of corruption and unceremoniously ousted before the end of his four-year term.    

Since then, supporters of the populist, anti-American, former captain of Pakistan’s cricket team have flooded streets in protests that often turned violent. Mr. Khan demanded a new election before its scheduled November date, even as new corruption charges were brought against him. 

Following this week’s arrest at the Islamabad courthouse, Mr. Khan’s supporters once again flooded the streets. The new element was that, unlike at any time in past protests, the military became a target. At least five people were killed while rioters stormed military buildings and ransacked the residence of a top army general at Lahore. The government called on the army to end the mayhem, but the Khan supporters were in no mood to comply.

“There are credible reports of differences among senior officers on how Imran Khan has been treated and the violations of the constitution and rule of law to serve the ambitions of a few,” a former American ambassador to the United Nations, Afghanistan-born Zalmay Khalilzad, tweeted on Wednesday. “Murdering Imran Khan will make things a lot worse in the country.”  

Following Thursday’s court ruling, Pakistanis are hoping rumors, violence, and clashes will end. Yet, a dam was broken. Ending the growing enmity between Mr. Khan and his supporters on the one hand, and the government of Premier Shebaz Sharif and the military on the other, will be difficult. It is far from clear that this time the military will prevail. 

“The last couple of days have seen extraordinary violence by protesters who are supporters of Imran Khan, who are obviously enraged by the manner in which he was arrested,” a former Pakistani ambassador to America, Maleeha Lodhi, told the BBC on Thursday. “There is still uncertainty, but hopefully the situation will not return to the kind of violent scenes that we have seen.” 

Ms. Lodhi added that Mr. Khan should concentrate on his demand to conduct an early election, rather than deepen his dispute with the army.

Yet, as the Manipal Academy’s Mdhav Das Nalapat told the Sun in March, “Khan is the first Pakistani politician to scold the military.” The military establishment represents mostly the Punjab province, he noted, while the rest of Pakistan’s tribal society may be rebelling. Such tribal enmity may be what Mr. Khan has tapped into.  

For America, Pakistan’s latest challenge presents a dilemma. “America got in bed with Pakistan decades ago, and we have no idea how to get out of it,” Mr. Newsham, a retired Marine colonel, says. The country and its military have never been true allies. They built up Islamist extremist groups, hosted Osama bin Laden, cultivated  deep hatred of India, and allied with Communist China.

As Washington tightens relations with New Delhi and sees it as a buffer against Beijing, a temptation will likely grow to cut ties with Islamabad. Yet, divorcing an increasingly chaotic nuclear-laced country may prove quite tricky.