[4] On 14 October, General Musharraf, acting as the country's Chief Executive, issued a controversial provisional order that suspended the Constitution of Pakistan.

[6] 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.

[10]: 167–168 [11]: 73–74  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.

[13] In light of the Supreme Court's verdict, the national referendum was held on 30 April 2002, allowing himself to continue his rule,[14][15] but was alleged by many (including the Human Rights Commission of Pakistan) to be fraudulent.

In 2007, President Musharraf eventually imposed another martial law by having suspended the populist Chief Justice IM Chaudhry, leveling charges of corruption and misconduct.

[20] 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.

[21]: 45–46  Prime Minister Sharif reacted angrily to the Court's actions, by issuing an intemperate public diatribe particularly against Chief Justice Shah.

[22]: 190  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.

[29]: 150–151 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.

[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.

[37]: contents [38] 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.

[39] 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.

[41] 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.

Ultimately, Prime Minister Sharif dismissed General Musharraf from the command of the military and nominated Lieutenant-General Ziauddin Butt, the DG ISI, over several army officers on 12 October 1999.

[47] When this was failed to comprehend by the pilot, the CAA was ordered to close the runways by turning off the edge lights at the Jinnah International Airport in an attempt to refuse the landing.

All persons who, immediately before the commencement of this Order, were in the service of Pakistan as defined in Article 260 of the Constitution and those persons who immediately before such commencement were in office as Judge of the Supreme Court, the Federal Shariat Court or a High Court or Auditor-General or Ombudsman and Chief Ehtesab Commissioner, shall continue in the said service on the same terms and conditions and shall enjoy the same privileges, if any.Upon hearing the news of Sharif's arrest, the PML(N) partisans and the party leadership led by Javed Hashmi, a conservative politician in Lahore and Mamnoon Hussain in Karachi called out and led massive street demonstrations and protests in the streets of Lahore, Karachi, and other cities.

[8]: 56–57  Eventually, the military court's inconclusive rulings found him to be guilty and convicted him for risking the life of all the passengers on board including the sitting Chairman joint chiefs.

[8]: 57 On 15 November 1999, the Supreme Court of Pakistan decided to hear the petitions filed by PML-N's lawyer Zafar Ali Shah on behalf of Sharif and Aitzaz Ahsan requesting a supreme court's intervention to declare the military takeover "illegal and unconstitutional", and order the restoration of Sharif's government and reinstatement of the National Assembly and four provincial assemblies that were suspended.

[58] As the hearing progressed at the Supreme Court, the legality and legitimacy of the coup became an important issue while Sharif's lawyers successfully argued for reinstating the writ of the constitution.

[4] Asma Jahangir, a Pakistani lawyer and human rights advocate, reportedly stated: "The military rulers are doing their best to erode the independence of the judiciary.

[61]: 366 In 2016, Musharraf later confessed in an interview given to Kamran Shahid of Dunya that "he pardoned Nawaz Sharif from life imprisonment on the request of King Abdullah and Rafic Hariri".

"[14] The credibility of the claims of illegitimacy is added when American Pattan Development Organization conducted a Gallup survey that founded that the "people are likely to elect either Benazir Bhutto or Nawaz Sharif as the next prime minister" in preference to President General Pervez Musharraf.

[40]: 111  It is claimed by authors that Prime Minister Sharif had well political intelligence on Musharraf's intention and had sought US President Bill Clinton's help against the military intervention.

[66]: 63–64 In 1999, Benazir Bhutto held all blames on Nawaz Sharif for the military takeover and criticized him stating "the man is violating every rule of law and, there is no-one to stop him.

"[67] In 2002, Admiral Bokhari quoted that: he knew about General Musharraf's plans to topple [Prime Minister] Nawaz Sharif and did not want to be part of these "Dirty Games".

[68] Admiral Bokhari also noted that a power struggle between an elected Prime Minister and appointed-Chairman joint chiefs ensued and relations were severely damaged after the Kargil war.

[70]: 76 In 1999 and in 2004, Sharif extended his apologies to various journalists and reporters for any wrongdoings and worked towards mending better relations with influential conservative news media after his exile.

[72] In 2006, the PML(N) issued a white paper concerning the Kargil events and Nawaz Sharif personally apologized to former Chief Justice Sajad Ali Shah and the former president Farooq Leghari for his role and his party's actions.

General Shahid Aziz was retired in 2004 as Lt-Gen.[75]: 184 [76]: 156 On 17 December 2019, Musharraf was handed the death sentence for treason by a three-member bench of a special court in Pakistan.