A top radical cleric of Islamabad's Lal Masjid, who led the holed up militants inside the pro-Taliban mosque in a tense week-long stand-off, was on Tuesday killed along with 88 of his associates.
Pakistani troops stormed the premises to flush out heavily-armed hardliners holding a large number of women and children as hostages.
Twelve commandos were also killed during Operation Silence, launched at 0400 hours after talks failed.
At least 88 militants, apart from cleric Abdul Rashid Ghazi, were killed in the operation, DawnNews TV quoted defence officials as saying.
43-year-old Ghazi, the younger brother of the captured head of the Lal Masjid Maulana Abdul Aziz, was killed by security forces in the basement after he refused to surrender, Interior Ministry spokesman Brig Iqbal Cheema said, nearly 16 hours after the operation was launched.
There were reports that Ghazi was holding women and children as human shields, some of whom were said to have been killed.
Officials added that Ghazi was shot in the leg and told to surrender, but he refused to do so.
The death toll has crossed 100 as the operation continued with well-armed militants engaging troops in pitched battles, according to latest reports.
"Troops are involved in room-to-room fighting to take control of layers and layers of the sprawling complex in central Islamabad," Pakistan Army spokesman Maj Gen Waheed Arshad said.
Arshad had earlier said Ghazi was located hiding in a deep bunker and was given a warning to surrender.
Troops took into custody Umme-e Hassan, Ghazi's sister-in-law and the principal of girls' madrassa attached to the mosque, and her daughter Asma. They also rescued about 134 people.
Earlier, Arshad said 50 militant students, including 34 children, surrendered on Tuesday morning, while 50 ultras who were injured were admitted to hospitals.
Replying to a question on why the operation took so long, Arshad said troops followed a step-by-step approach to minimise the casualties.
He said the complex has over 75 rooms besides vast courtyards and basements and all needed to be cleared one by one and that there were still some bunkers to be cleared.
There are reports that more women and children were locked up in the basement and troops are trying to verify it.
Arshad denied reports that the Pakistan army planned to use nerve gas against militants. The Pakistan army had no stocks of the nerve gas, he said.
Umme-e Hassan, who was taken into custody along with her daughter Asma, had a few days ago attempted to help her husband Maulana Aziz to flee from the mosque wearing a burqa, but he was identified and arrested.
Ghazi had not even allowed his ailing mother to come out and undergo treatment, Arshad said.
With Tuesday's operation, curtains finally came down on the six-decade-old Lal Masjid's red brand of Islam as well as its six-month long moral brigade activities to impose Shariah law.
The army raid took place in a dramatic fashion after an 11-hour "cell phone" talks between Ghazi and Shujaat Hussain, the former premier and chief of ruling Pakistan Muslim League-Q, failed to end the stand-off.
"I have never been disappointed in my life, but I am leaving this place with extreme dejection," Hussain said in the nationally-televised press meet after the talks failed.
"I asked him to give up his stubborn attitude for the sake of Allah, for the sake of children, for the sake of women, sisters and mothers, but in vain," Hussain said.
By the time the dazed newsmen, who till then perceived that a breakthrough was round the corner, absorbed Hussain's statement, firing and explosions rocked many sides of the Lal Masjid and the defence ministry lost no time in announcing that Operation Silence, the code name for action against the mosque, had commenced.
Ghazi, taking advantage of the cell phone handed over to him by the government for talks, quickly called the channels in the midst of the explosions claiming that he had been deceived by Hussain and Religious Affairs Minister Izajul Haq and vowed to resist the crackdown till his death.
"I said to Shujaat [Hussain] that kill us, but people will not allow you to go in peace," Ghazi said before the government disconnected his phone.
Commenting on the Operation Silence, Ghazi said, "This is gross injustice; the people conducting the operation are American agents and carrying out this operation on the US' bidding. Now I am sure to be a martyr soon."
It is not yet clear what kind of fallout this operation and Ghazi's death would have on President Pervez Musharraf's future.
The operation is, however, expected to win Musharraf more international support.
Musharraf, the chief of army, has survived many close bids on his life, including by suicide bombers. The attempt to blow up his plane a few days ago in Rawalpindi also failed.
Tuesday's operation followed a stern warning from Musharraf to Ghazi and his followers to either surrender or die.
The operation formally ended the reign of Ghazi brothers -- Aziz and Rashid -- whose family headed the mosque ever since their father Abdullah was appointed its head priest by Pakistan's first military ruler Ayub Khan when it was constructed in 1965.
Since then it remained a patron of all military rulers, especially Zia-ul Haq, and even under Musharraf it continued to have links with Al Qaeda and the Taliban.
Abdullah died in 1998 but his sons, however, continued promoting radical views.