[11] After the Soviet–Afghan War ended in 1989, the mosque continued to function as a centre for Islamic extremist learning and housed several thousand male and female students in adjacent seminaries.

[13] During 2006 and the first half of 2007, students and mosque leaders continued to challenge the Pakistani government's authority by calling for Islamic law and to end co-operation with the United States.

[14] Students at the Red Mosque's two affiliated seminaries launched a campaign for Shari'a, occupying a nearby children's library and embarking on vigilante raids through the capital to stop what they called "un-Islamic activities," such as DVD vendors, barber shops and a Chinese-run massage parlor that they accused of being a brothel.

On 6 April, Abdul Aziz established a sharia court in parallel with Pakistan's federal judicial system and pledged thousands of suicide attacks if the government attempted to close it.

Government authorities announced the first deadline for the occupants of Lal Masjid to surrender unconditionally as 15:30 Pakistan Standard Time (PST), and it was pushed back to 16:00, 18:00, 19:30 and then 21:30.

Interior Minister Aftab Ahmad Sherpao announced at a press conference that the government believed that between 300 and 400 students remained in the mosque, and only 50 to 60 were considered to be militants.

[23] Pakistani commandos raided the outer perimeter of the compound, blasting holes through the walls of the mosque to allow trapped women and children to escape.

On 9 July 2007, a group representing Pakistani madrasahs, headed by Maulana Salimullah Khan, called for an immediate cessation of the Lal Masjid operation.

Analysts suggest that it may have been retaliation for ongoing operations against Lal Masjid and the government's continued efforts to combat terrorism and Talibanization in northern Waziristan.

Predator unmanned aerial vehicles flew over Lal Masjid and Jamia Hafsa on 8 and 9 July 2007, capturing images of the deployment of people inside.

[28] Security forces had the images taken to study the claims of Ghazi Abdul Rashid regarding casualties and damage caused to Lal Masjid and Jamia Hafsa.

[30] After the minarets were taken, the Special Service Group progressed deeper into the complex, and the militants threw gasoline bombs in an unsuccessful attempt to set fire to the mosque and stop the assault.

[30] Once the ground floor was secured, the Special Service Group attempted to enter the Jamia Hafsa madrasah adjoining the mosque but were delayed by booby traps, which had to be disabled before they could continue into the complex.

[30] The Special Service Group entered the complex, in order to take over the control of Jamia Hafsa which also served as Abdul Rasid Ghazi's living quarters, and engaged in a firefight in the main courtyard.

In a last interview with Geo TV during the operation, Abdul Rashid Ghazi, who was hunkered down in the basement, claimed that his mother had been wounded by gunfire and was quoted as saying: "The government is using full force.

The Associated Press reported: "The siege has given the neighborhood the look of a war zone", with troops manning machine guns behind sandbagged posts and from the top of armoured vehicles.

[30] Intelligence agencies expressed shock at the highly sophisticated weapons that the militants in the Lal Masjid and Jamia Hafsa compound had, and began an investigation into where the equipment came from.

[30] Officials in Islamabad considered the operation a success, citing that they were able to subdue all the fighters inside the mosque—a group that allegedly included foreign terrorists—without a heavy civilian toll.

[41] Securing Lal Masjid brought an end to nine days of high tension in Islamabad, normally a tranquil city that had been immune to the violence experienced in the tribal areas of Pakistan.

[48] Pakistani intelligence officials said they found letters from Osama bin Laden's deputy, Ayman al-Zawahiri, after taking control of Lal Masjid.

Government sources believe that as many as 18 foreign fighters from Uzbekistan, Egypt, and Afghanistan had arrived weeks before the final confrontation and established firing ranges to teach the students, including children, how to handle weapons properly.

[49] Al-Qaeda's second-in-command, al-Zawahiri, issued a videotape on 11 July 2007, calling for Pakistanis to join jihad in revenge for the attack by the Pakistan's Army on the mosque.

But this was not done and, for the first time in the history of Pakistan, our own security forces not only bombarded a mosque and religious seminary, but also brought in armored personnel carriers, tanks and helicopter gunships in numbers that made you wonder.

"[53] The Ausaf daily countered, "The entire nation is grieving ... only the United States wanted what happened and proof of that is that the storming operation was celebrated at the White House and Pentagon rather than at General Musharraf's headquarters.

[55] The European Union President, José Manuel Barroso, issued a statement that it "supports the Government of Pakistan in the defense of the rule of law and the writ of the State against the threat posed by such armed radical groups in the context of the fight against extremism.

"[59] Religious parties and figures criticised the support extended by the U.S. consular official and demanded that the government expel him for interfering in Pakistan's internal affairs.

A Pakistani Foreign Office spokesperson Tasneem Aslam characterised the U.S. consulate official's statement as contrary to diplomatic norms, and open interference in the country's internal affairs.

[60] On 16 August 2007, acting on a suo motu notice, the Supreme Court of Pakistan took up the extrajudicial killings of the people at the Lal Masjid and Jamia Hafsa complex.

[61] Mohammed Ahsan Bhoon, president of the Lahore High Court Bar Association, said, "This issue could have been resolved through negotiations but General Musharraf intentionally spilled the blood of innocent people to please his foreign masters.

[64] In February 2016, a local courts judge issued non-bailable warrants for the arrest of Musharraf for his 'deliberate' absence from the proceedings of the murder case of Lal Masjid cleric Abdul Rashid Ghazi.