The 1999 military takeover in Pakistan was a bloodless coup d'état initiated by the military staff at the Joint Staff HQ working under the Chairman of the Joint Chiefs of Staff Committee and Chief of Army Staff General Pervez Musharraf. The instigators seized control of the civilian government of the popularly elected Prime Minister Nawaz Sharif on 12 October 1999. On 14 October, General Musharraf, acting as the country's Chief Executive, issued a controversial provisional order that suspended the Constitution of Pakistan.

Martial law was declared due to the breakdown of civil-military relations. Tensions between the Sharif administration and joint chiefs chairman General Musharraf reached a breaking point. In an attempt to maintain civilian control over the military, Lieutenant-General Ziauddin Butt, then Director of the ISI, was hastily approved for the appointment of the army chief, but the decision was opposed by senior members of the Joint Staff HQ, who refused to follow the new chain of command, deciding instead to direct the Military Police to detain General Butt and prevent his taking control of the military.

The pace of the coup startled political observers; within 17 hours of Sharif's attempt to relieve General Musharraf, army commanders took control of all key government institutions throughout the country and placed Sharif and his administration, which included his brother, under house arrest. Military police took control of the state broadcaster, radio and the entire critical communications infrastructure, and announced that Sharif had been dismissed.

The Supreme Court of Pakistan led by Chief Justice Irshad Hassan Khan validated the martial law under a "doctrine of necessity" but limited its legality to three years. Meanwhile, Sharif was tried by the Judge Advocate General Court and convicted of endangering the lives of all passengers aboard the aircraft carrying Musharraf, with the military court upholding the decision. When the decision was announced, it sparked fury in the conservative PML(N) but was welcomed by many of its political opponents. In 2000, the Supreme Court accepted arguments that the coup was a "violation of the constitution". However, acting Chief Justice Ershad Hasan later argued of the constitutionality of the coup.

On 10 December 2000, Musharraf unexpectedly issued a pardon to Nawaz Sharif to be flown to Saudi Arabia. In 2016, Musharraf later confessed in an interview given to Kamran Shahid of Dunya that "he pardoned Sharif from life imprisonment on the request of King Abdullah and Rafic Hariri."

In 2001, Musharraf issued the executive decree and eventually forced President Rafiq Tarar to resign in order for Musharraf to assume the presidency. In light of the Supreme Court's verdict, the national referendum was held on 30 April 2002, allowing himself to continue his rule, but was alleged by many (including the Human Rights Commission of Pakistan) to be fraudulent. In 2002, the general elections restored democracy when the Musharraf-backed PML(Q), the libertarians, were able to form a minority government who would later nominate Musharraf for the 2004 presidential elections. In 2007, President Musharraf eventually imposed another martial law by having suspended the populist Chief Justice IM Chaudhry, leveling charges of corruption and misconduct. Unlike the earlier martial law, Musharraf was widely disapproved, inviting mass demonstrations led by Nawaz Sharif, Musharraf eventually resigned in an attempt to avoid impeachment in the Parliament.

Sharif was acquitted in 2009 from the 1999 hijacking case and in 2014 acquitted of the money laundering and corruption cases from an accountability court.

Events leading towards the martial law Relief of General Jehangir and Kargil debacle

In 1997, Nawaz Sharif and his conservative Pakistan Muslim League-N won a landslide victory in the general elections, resulting in a two-thirds majority in the National Assembly– the lower house of bicameral Parliament of Pakistan.

His second tenure was marked with a serious legal confrontation with the Supreme Court courted by Chief Justice Sajjad Ali Shah over the legality and technicality of Thirteenth Amendment and the Ehtesab Act, 1997 (lit. Accountability Act, 1997). Chief Justice Shah had been battling in the Supreme Court for his legitimacy due to many senior justices had seen his appointment as "inappropriate and political", having been appointed by former prime minister Benazir Bhutto in 1994. On 29 October 1997, Chief Justice Shah and his bench decided to hear the petition filed by the Pakistan Peoples Party's lawyers and suspended the implementation of bills. Prime Minister Sharif reacted angrily to the Court's actions, by issuing an intemperate public diatribe particularly against Chief Justice Shah. On 2 November 1997, Chief Justice Shah summoned Prime Minister Sharif for contempt of court but this order was viewed "null and voided" when two senior justices at the Supreme Court issued a counter-order. On 30 November 1997, Prime Minister Sharif appeared before the Supreme Court but his partisans stormed the Supreme Court Building forcing Chief Justice Shah to remove the finding of contempt against Sharif. While the police gained control of the situation to restore law and order, the whole nation witnessed traumatising and terrifying scenes on their television screens broadcast by the news media all over the country.

Subsequently, the Supreme Judicial Council took up a case against the appointment of Chief Justice Shah on 23 December and declared Chief Justice Shah's appointment "illegal and unconstitutional" that eventually forced him to resign from his office on 2 December 1997. President Farooq Leghari who supported the cause of Chief Justice Shah also had to resign when army chief General Jehangir Karamat and Chairman joint chiefs Air Chief Marshal Feroze Khan intervened to resolve the crises. Prime Minister Sharif eventually appointed his Chief Justice Saeeduzzaman Siddiqui based on merit qualification and offered presidency to former supreme court justice Rafiq Tarar who was elected in 1998.

In 1998, Prime Minister Sharif effectively relieved Chairman Joint Chief of Staff Committee General Jehangir Karamat from the command of the military when General Karamat delivered a college lecture at the Naval War College in Karachi. At this lecture, General Karamat called for establishing the National Security Council (NSC) which would be backed by a "team of civil-military experts" for devising policies to seek resolution ongoing problems relating the civil-military issues; also recommended a "neutral but competent bureaucracy and administration of at federal level and the establishment of Local governments in four provinces.

Relieving of General Karamat plummeted Sharif's own public approvals and his relations with the military, as even his senior Cabinet ministers were in disagreement of Sharif's decision. Many political observers were taken in complete surprise since the dismissal of four-star rank general had never happened before in country's history.

Eventually, Sharif chose then-Lieutenant-General Pervez Musharraf over two senior army generals for the appointment to post of the army chief and acting Chairman Joint Chief of Staff Committee. A year later, the civil military relations took a sharp turn in the opposition of Sharif when he invited and received Indian Prime Minister Atal Vajpayee in Lahore for peace talks, much to agitation of General Musharraf who did not welcome outcomes of Lahore Summit.

In 1999, the Pakistan Army soldiers secretly crossed the Line of Control (LoC) and infiltrated in Kargil on the direct orders issues by General Musharraf, bringing the two nations at the brink of war. The Indian Army reacted with launching of full-fledged military coordinated operations while Indian government effectively put diplomatic pressure on Sharif's government to withdraw the soldiers from the Kargil sector.Weaver, Mary Anne. "General on Tightrope". Pakistan: In the Shadow of Jihad and Afghanistan. New York: Farrar, Straus and Giroux, 2003. pp. 25–31. . Both Sharif and General Musharraf held each other responsible for the actions in the Kargil sector, charging each other of lying and hiding details of the hostilities to the nation.

At the public circle, Sharif assigned blame for the political/diplomatic disaster on General Musharraf, and Musharraf placing the blame on Prime Minister Sharif. In September 1999, General Musharraf forcefully retired Lieutenant-General Tariq Pervez who was known to be close to Sharif and cousin of Raja Nadir Pervez, the Communications Minister.

Upon meeting with Sharif, General Tariq Pervez had ultimately warned Sharif of "making any move against General Musharraf or the army would strike."

Revolt of the Admiral The revolt of Admiral Fasih Bokhari, the Chief of Naval Staff, over Sharif's public decision of extending General Musharraf's tenure as Chairman Joint Chief of Staff Committee until 2001 was another issue that saw the breaking down of civil-military relations. About the Kargil war, Admiral Bokhari was not of the view of supporting the Pakistan Army's engagement with the Indian Army as appropriate and subsequently lodged a powerful protest against General Musharraf's grand strategy while recommending the constitution of a commission to completely probe the Kargil issue.

At the country's news media, Admiral Bokhari publicly questioned the effectiveness of the military strategy behind the Kargil infiltration and was very critical of General Musharraf's unilateral decisions involving the national security, as Chairman Joint Chief of Staff Committee, without considering the opinions of Chiefs of Staff of Pakistan Air Force and the Pakistan Navy.

In 1999, Sharif quarrelled with Admiral Bokhari and his Navy NHQ staff over the merit-based appointment of General Musharraf to the Chairman Joint Chiefs that was only meant to be temporary and it was hoped that Admiral Bokhari would be appointed to the post. In August 1999, there were rising tensions between Admiral Bokhari and Prime Minister Sharif over issue of incident took place in Sir Creek, although both had kept the working relations on good terms.

In September 1999, General Musharraf had sent a message to Prime Minister Sharif that "anyone in the Navy and Air Force can become the Chairman Joint Chiefs as I did not care." General Musharraf reportedly backed Admiral Bokhari's bid for the Chairman Joint Chiefs but he was overshadowed by the Prime Minister who confirmed and extended General Musharraf's term until 2001.

Civil-military relations were further damaged when Admiral Bokhari lodged a strong protest against this decision in the news media and reportedly revolted against Prime Minister Sharif's appointment for the Chairman Joint Chiefs in 1999. Admiral Bokhari abruptly tendered his resignation to the Prime Minister Sharif and noted to Sharif that since General Musharraf was his junior and often referred to him as "Sir".

On 5 October 1999, Admiral Bokhari resigned from the command of the Navy as the news media construed Admiral Bokhari's resignation merely as unhappiness over not being appointed as Chairman of the Joint Chiefs of Staff Committee. Admiral Bokhari's revolt saw the meltdown of the civil-military relations between the elected civilian government and the military leaders that eventually led to the military overtaking the civilian government by dismissing Prime Minister Sharif on 12 October 1999.

The military takeover

In the aftermath of the Kargil War, followed by the Atlantique incident, there were widespread rumors and media speculations in the television news media about the either possible military takeover or resignation of General Musharraf in September 1999.