ISLAMABAD, Pakistan -- In a sudden erosion of military privilege and impunity, a Pakistani court indicted the former ruler Pervez Musharraf on Tuesday in connection with the 2007 assassination of former Prime Minister Benazir Bhutto – the first time that such a senior general has faced criminal charges.
The court filed three charges against Mr. Musharraf, 70, including murder and conspiracy to murder, said a prosecutor, Chaudhry Muhammed Azhar. He spoke after the court's brief hearing in the garrison city of Rawalpindi. Reporters were excluded from the hearing.
Mr. Musharraf, who had previously claimed the case against him was politically motivated, pleaded not guilty, his lawyers said. Afterward, police commandos and paramilitary rangers escorted him back to his villa on the edge of the capital, Islamabad, where he has been under house arrest since April in connection with other cases stemming from his rule, from 1999 to 2008.
The symbolism of a once untouchable general being called to account was potent in a country that has been ruled by the military for about half of its 66-year history. While the military remains deeply powerful, the prosecution of Mr. Musharraf signaled that even Pakistan's top generals are sometimes subject to the rule of law -- at least after they have retired.
Mr. Musharraf did not speak to reporters as he left the hearing, surrounded by a phalanx of security guards. His spokesman, Reza Bokhari, later called the charges "false, fabricated and fictitious" and said they represented "an undignified attempt to smear the honor and integrity of the former president."
Mr. Musharraf's indictment spurred skepticism among some Pakistanis, who saw it as a moment of political revenge and misleading clarity in a case still clouded by confusion, obfuscation and the mysterious deaths of potential witnesses and prosecutors over the years.
Indeed, prosecutors have publicly disclosed little detail about how Mr. Musharraf might be linked to Ms. Bhutto's death. The new charges are believed to rely heavily on a statement by Mark Siegel, a Washington lobbyist and friend of Ms. Bhutto, who said that Mr. Musharraf made a threatening phone call to her before she returned to Pakistan in October 2007.
Mr. Siegel said Ms. Bhutto had warned him in an e-mail that if she were killed, the blame should fall on four named people -- a former director of the Inter-Services Intelligence Directorate, Pakistan's main spy agency; a military intelligence chief; a rival politician; and Mr. Musharraf, who was then president and army chief.
Two months later, Ms. Bhutto was killed during a gun and bomb attack as she left a rally in Rawalpindi. Mr. Musharraf's government quickly blamed Baitullah Mehsud, the leader of the Pakistani Taliban. Weeks later, the head of the Central Intelligence Agency at the time, Michael V. Hayden, agreed with that assessment.
"We have no reason to question that," Mr. Hayden told The Washington Post. Eighteen months later, the C.I.A. killed Mr. Mehsud in a drone strike in the tribal belt.
The court action on Tuesday provided the most dramatic chapter yet in a steep fall from grace for Mr. Musharraf, a swaggering, whiskey-swilling general who seized power in 1999. Over his nine-year rule he became a crucial ally of the United States and escaped several Al Qaeda assassination attempts -- all the while pursuing an ambiguous policy toward other jihadi groups, including the Afghan Taliban.
Sweeping street protests, led by lawyers, forced Mr. Musharraf to step down in 2008, and he fled into exile in London and Dubai.
To a large degree, he has brought his recent misfortunes upon himself. Against the advice of many aides, including senior generals, he returned to Pakistan from exile this year in the hope of contesting elections and resurrecting his dormant political career, vowing the save the country from chaos.
But instead of receiving a hero's welcome, Mr. Musharraf was mocked by political rivals, mostly ignored by the media and collared by the courts, which are controlled by his old rival, Chief Justice Iftikhar Muhammad Chaudhry -- the famously stubborn judge who had led the protest movement against Mr. Musharraf in 2007.
The courts have revived charges against Mr. Musharraf in four cases. But it is the Bhutto prosecution, and a potential treason prosecution, that are mostly like to strain relations among the country's judicial, political and military leaders.
The treason prosecution is supported by Prime Minister Nawaz Sharif, whose last stint in power ended in 1999 after he was ousted by Mr. Musharraf in a coup. But inside the military, the prospect of a former military chief facing a potential death penalty has caused simmering anger.
The Bhutto case, meanwhile, has become embroiled in bitter contention and violent intrigue. Apart from Mr. Musharraf, six other people were also indicated at Tuesday's court hearing, including two senior police officers who face accusations that they sanitized the Bhutto crime scene.
A United Nations investigation, which published its findings in 2010, said that a senior unnamed army officer had ordered one of those police officers, a former Rawalpindi police chief, Saud Aziz, to hose down the scene in the hours after Ms. Bhutto's assassination.
The car in which Ms. Bhutto died was also cleaned out, destroying its evidential value.
"The police deliberately botched the investigation into Bhutto's assassination," wrote Heraldo Muñoz, a Chilean diplomat who led the United Nations investigation, in an article published this week.
The Pakistani investigation has also been hampered by political lethargy and several unexplained killings. Although Ms. Bhutto's widower, Asif Ali Zardari, became president of Pakistan in 2008, he never showed much enthusiasm for the investigation. That same year, Ms. Bhutto's chief bodyguard, Khalid Shahenshah, was shot dead by unidentified gunmen in Karachi.
And in May the chief prosecutor in the case, Chaudhry Zulfikar Ali, was gunned down in his car as he drove to work in Islamabad.
For his part, Mr. Musharraf also has major security concerns. The Pakistani Taliban have issued repeated death threats against him since his return to Pakistan. A previous court hearing, scheduled for Aug. 6, was postponed over fears for his life.
Now, the next hearing in the Bhutto case is scheduled for Aug. 27. The presiding judge, Habibur Rehman, accepted Mr. Musharraf's request that he not be required to appear personally.
As he waits, the once powerful leader may draw cold comfort from Mr. Muñoz, the United Nations diplomat, whose forthcoming book "Getting Away with Murder" concludes that, despite her e-mail to the contrary, Ms. Bhutto probably did not believe that Mr. Musharraf wanted to kill her -- "only that some people around him did."
Salman Masood reported from Islamabad, and Declan Walsh from London.
This article originally appeared in The New York Times.