Commandos cleared the warren-like Red Mosque complex of rebel fighters Wednesday, ending a fierce eight-day siege and street battles that left more than 100 dead. The government warned it would not tolerate militancy in any of Pakistan's thousands of religious schools.
Hours later, deputy al Qaeda leader Ayman al-Zawahri released a video calling for Pakistanis to wage holy war against their government in retaliation for the assault.
The video was released by al Qaeda's multimedia branch, as-Sahab. Its authenticity could not immediately be confirmed, but two U.S.-based terrorism monitoring groups also reported it.
Officials searching the mosque after the assault found no corpses of women and children, although seven or eight of the bodies had been burned beyond recognition, apparently by the militants' gasoline bombs, said Maj. Gen. Waheed Arshad, a military spokesman.
At least 106 people were killed overall since the violence began at the Red Mosque. They included 10 soldiers, one police ranger and several civilians who died in the crossfire in the initial street fighting last week.
Among the dead was the mosque's pro-Taliban cleric, Abdul Rashid Ghazi.
Arshad said 73 bodies believed to be those of the mosque's die-hard defenders were found after the final, 35-hour assault that began early Tuesday.
"There may be a few more which may be found in the debris. We don't expect there will be many," Arshad told Dawn News television. "We have handed them (the bodies) to the civilian authorities."
The elite Special Services Group commandos went in after unsuccessful attempts to get the militants to surrender to the siege mounted by the government following deadly street clashes with armed supporters of the mosque July 3.
The extremists had been using the mosque as a base to send out radicalized students to enforce their version of Islamic morality, including abducting alleged prostitutes and trying to "re-educate" them at the compound in the heart of Pakistan's capital.
Prime Minister Shaukat Aziz warned that the government would act against any other madrassa, or religious school, found to be involved in militancy.
"Militancy cannot be promoted, period," he told reporters. "The law will take its course, as the law took its course here."
President Gen. Pervez Musharraf vowed five years ago to regulate Pakistan's thousands of religious schools, but concerns have only grown that some are used as sanctuaries or training sites for militants — including Taliban rebels fighting in Afghanistan.
Deputy Information Minister Tariq Azim conceded it was possible that other madrassas in Pakistan could be harboring weaponry like the Red Mosque, but added that the assault had sent a strong message that the government "meant business."
"We need to be now much more vigilant, but I hope they (extremist madrassas) have got the message that if they are in involved in such activities, they will have to face action," he said.
An army officer, who spoke on condition of anonymity because he was not authorized to speak to the media, said troops moved from room to room in basements of the compound, blowing up foxholes where militants had been entrenched.
Relatives of young women, men and children who had been in the mosque waited behind army barricades and inquired at morgues or a sports stadium where authorities set up an information center for those seeking missing loved ones.
"I am looking for my son who was studying at the madrassa, but I don't know whether he is alive," said Jan Mohammed, 42, whose son, Mohammed Khan, could not leave the mosque during the siege. He was among about 100 parents who were gathered at the sports stadium.
Ghazi's body was found in the basement of a women's religious school after a fierce gunbattle between government troops and militants, said Brig. Javed Iqbal Cheema, a senior Interior Ministry official.
Several security officials, who spoke on condition of anonymity because they were not authorized to speak to the media, said Ghazi was wounded by two bullets and gave no response when ordered to surrender. Commandos then fired another volley and found him dead.
Arshad said Ghazi's body had been handed over to the Interior Ministry.
Cheema said the body was taken for burial in Ghazi's native village of Rojhan in southwestern Pakistan. His brother, Abdul Aziz, the mosque's chief who was arrested trying to escape from the complex last week, would be allowed to attend the funeral.
The military announced that about 1,300 people had escaped or otherwise left the compound since July 3. Authorities took an unknown number into custody, while others, mostly young students, have returned to their homes.
Arshad said the media would be taken on a tour of the mosque complex, but probably not until Thursday.
The casualties at the Red Mosque could further turn public opinion against President Gen. Pervez Musharraf, who already faces a backlash for his bungled attempts to fire the country's chief justice.
Following several fiery anti-government protests Tuesday, about 500 people chanting "Death to Musharraf!" rallied for an hour Wednesday in the northwest frontier city of Peshawar.
"This (mosque attack) is part of our government's action against religious elements to please America," said Shabbir Khan, a lawmaker from an opposition Islamic party, at the demonstration.
About 15 other Islamic opposition lawmakers gathered in front of the Supreme Court in Islamabad, blaming Musharraf for Pakistan's troubles, including the mosque attack, and calling for his resignation.
Anger over the siege also reached fundamentalist Islamic communities far from the region.
Anjem Choudary, whose group held the rally against "the apostate regime of Pervez Musharraf," shouted to the crowd gathered in central London, "Where are the Islamists? Let them come and demonstrate."
Choudary told CBSNews.com that the government had "bombed innocent women and children" inside the Red Mosque complex, and the only weapons held by the people inside had been licensed guns.
When asked about the mosque's members kidnapping people off the streets of Pakistan, Choudary said, "They didn't kill them, they removed them. It was absolutely correct."
Choudary's hardline group advocates Sharia, or Islamic, Taliban-style rule, for Pakistan and across the Muslim world. "As Muslims, we abide by the Sharia, even if the government doesn't. It is our responsibility to make sure it is implemented. We follow the Prophet Mohammed, not Musharraf."
To the idea that it was the people of Pakistan's responsibility to instigate change in the way the country was led by political means, Choudary said: "We don't believe in those concepts of Democracy and liberalism … It's not about the majority, forget the minority and majority."
Though Choudary's views mirror those espoused by radical Islamic groups around the world, he conceded that Pakistan was not likely to fall to a Taliban-style government any time soon.
"That is what we are striving for," he said. Choudary said his group did not endorse militant action in the West, but that if extremists came from Pakistan to attack London, the blood would be on the hands of the British government, and "we cannot be held responsible."
In Afghanistan, a senior Taliban commander, Mansoor Dadullah, urged Muslims to launch suicide attacks on Pakistani security forces, calling the assault "a cruel act."
"I would have sent 10,000 mujahedeen to support the (Red Mosque) students but we are busy in Afghanistan and Islamabad is far from Afghanistan. I wished to go myself to support them," he told The Associated Press by telephone.
Several editorials in mainstream newspapers said Musharraf had no choice but to confront the militants.
"The decision to launch the final assault was not an easy one, but given the circumstances there was nothing else that the government could really do," said the English-language paper The News.
But it questioned how the militants had managed to find a haven "inside the heart of Islamabad."
"Surely this is a disturbing indictment of the failure of the law enforcement agencies to keep track of the movement of such elements," it said.
Another English-language daily, Dawn, said that "no tears will be shed over the death of the well-armed militants," praising the government for exercising "utmost restraint" in the standoff.
The State Department endorsed the Musharraf government's decision to storm the mosque, saying that the militants had been given many warnings, and President Bush reaffirmed his confidence in the Pakistani president in the fight against extremists.