Third military era (1999 - 2007)

On 12 October, 1999, Sharif attempted to dismiss army chief Pervez Musharraf and install ISI director Ziauddin Butt in his place, but senior generals refused to accept the decision.[73] Musharraf, who was out of the country, boarded a commercial airliner to return to Pakistan. Sharif ordered the Jinnah International Airport to prevent the landing of the airliner, which then circled the skies over Karachi. In a coup, the generals ousted Sharif's administration and took over the airport.[11] The plane landed with only a few minutes of fuel to spare, and General Musharraf assumed control of the government. He arrested Sharif and those members of his cabinet who took part in this conspiracy. American President Bill Clinton had felt that his pressure to force Sharif to withdraw Pakistani forces from Kargil, in Indian-controlled Kashmir, was one of the main reasons for disagreements between Sharif and the Pakistani army. Clinton and King Fahd then pressured Musharraf to spare Sharif and, instead, exile him to Saudi Arabia, guaranteeing that he would not be involved in politics for ten years. Sharif lived in Saudi Arabia for more than six years before moving to London in 2005.

On May 12, 2000 the Supreme Court of Pakistan ordered the Government to hold general elections by October 12, 2002. In an attempt to legitimize his presidency[74] and assure its continuance after the impending elections, Musharraf held a controversial national referendum on April 30, 2002,[75] which extended his presidential term to a period ending five years after the October elections.[76] Musharraf strengthened his position by issuing a Legal Framework Order in August 2001 which established the constitutional basis for his continuance in office.[77] The general elections were held in October 2002 and the centrist, pro-Musharraf PML-Q won a majority of the seats in Parliament. However, parties opposed to the Legal Framework Order effectively paralysed the National Assembly for over a year. The deadlock ended in December 2003, when Musharraf and some of his parliamentary opponents agreed upon a compromise, and pro-Musharraf legislators were able to muster the two-thirds majority required to pass the Seventeenth Amendment, which retroactively legitimized Musharraf's 1999 coup and many of his subsequent decrees. In a vote of confidence on 1 January 2004, Musharraf won 658 out of 1,170 votes in the Electoral College of Pakistan, and according to Article 41(8) of the Constitution of Pakistan, was elected to the office of President.[78]

While economic reforms undertaken during his regime have yielded some results, social reform programmes and his liberal views, e.g. on reforming extremist versions of the practices prevalent in Islam, appear to have met with resistance. Musharraf's power is threatened by extremists who have grown in strength since the September 11, 2001 attacks and who are particularly angered by Musharraf's close political and military alliance with the United States, including his support of the 2001 invasion of Afghanistan. Musharraf has survived several assassination attempts by terrorist groups believed to be part of Al-Qaeda, including at least two instances where the terrorists had inside information from a member of his military security. Pakistan continues to be involved in a dispute over Kashmir, with allegations of support of terrorist groups being levelled against Pakistan by India, while Pakistan charges that the Indian government abuses human rights in its use of military force in the disputed region. What makes this dispute a source of special concern for the world community is, that both India and Pakistan possess nuclear weapons. It had led to a nuclear standoff in 2002, when Kashmiri-militants (supposedly backed by the ISI) attacked the Indian parliament. In reaction to this, serious diplomatic tensions developed and India and Pakistan deployed 500,000 and 120,000 troops to the border respectively.[79] While the Indo-Pakistani peace process has since made progress, it is sometimes stalled by infrequent insurgent activity in India (including the 11 July 2006 Mumbai train bombings). Pakistan also has been accused of contributing to nuclear proliferation; indeed, its leading nuclear scientist, Abdul Qadeer Khan, admitted to selling nuclear secrets, though he denied government knowledge of his activities.

After the U.S. led invasion of Afghanistan, the Pakistani government, as an ally, sent thousands of troops into the mountainous region of Waziristan in 2002, in search of bin-Laden (whom the U.S. blames for master-minding the 9/11-events) and other heavily armed al-Qaeda members, who had allegedly taken refuge there. In March 2004, heavy fighting broke out at Azam Warsak (near the South Waziristan town of Wana), between Pakistani troops and these militants (estimated to be 400 in number), who were entrenched in several fortified settlements. It was speculated that bin Laden's deputy Ayman al-Zawahiri was among those trapped by the Pakistani Army. On September 5, 2006 a truce was signed with the militants and their local rebel supporters, (who called themselves the Islamic Emirate of Waziristan), in which the rebels were to cease supporting the militants in cross-border attacks on Afghanistan in return for a ceasefire and general amnesty and a hand-over of border-patrolling and check-point responsibilities, till then handled by the Pakistan Army.

Former prime minister Nawaz Sharif attempted to return from exile on September 10, 2007 but was arrested on corruption charges after landing at Islamabad International Airport. Sharif was then put on a plane bound for Jeddah, Saudi Arabia, whilst outside the airport there were violent confrontations between Sharif's supporters and the police.[80] This did not deter another former prime minister, Benazir Bhutto, from returning on October 18, 2007 after an eight year exile in Dubai and London, to prepare for the parliamentary elections to be held in 2008.[81][82] However, on the same day, two suicide bombers attempted to kill Bhutto as she travelled towards a rally in Karachi. Bhutto escaped unharmed but there were 136 casualties and at least 450 people were injured.[83]

On November 3, 2007, General Musharraf proclaimed a state of emergency and sacked the Chief Justice of Pakistan, Justice Iftikhar Muhammad Choudhry along with other 14 judges of the Supreme Court.[84][85] Lawyers launched a protest against this action but they were arrested. All private media channels were banned including foreign channels. Musharraf declared that the state of emergency would end on December 16, 2007.[86] On November 28, 2007, General Musharraf retired from the Army and the following day was sworn in for a second presidential term.[87][88]

On November 25, 2007, Nawaz Sharif made a second attempt to return from exile, this time accompanied by his brother, the former Punjab chief minister, Shahbaz Sharif. Hundreds of their supporters, including a few leaders of the party were detained before the pair arrived at Lahore International Airport.[89][90] The following day, Nawaz Sharif filed his nomination papers for two seats in the forthcoming elections whilst Benazir Bhutto filed for three seats including one of the reserved seats for women.[91]

On December 27, 2007, Benazir Bhutto was leaving an election rally in Rawalpindi when she was assassinated by a gunman who shot her in the neck and set off a bomb,[92][93] killing 20 other people and injuring several more.[94] The exact sequence of the events and cause of death became points of political debate and controversy, because, although early reports indicated that Bhutto was hit by shrapnel or the gunshots,[95] the Pakistani Interior Ministry stated that she died from a skull fracture sustained when the explosion threw Bhutto against the sunroof of her vehicle.[96] Bhutto's aides rejected this claim and insisted that she suffered two gunshots prior to the bomb detonation.[97] The Interior Ministry subsequently backtracked from its previous claim.[98] However, a subsequent investigation, aided by the Scotland Yard of U.K., supported the "hitting the sun-roof"" as the cause of her death. The Election Commission, after a meeting in Islamabad, announced that, due to the assassination of Benazir Bhutto,[99] the elections, which had been scheduled for 8 January 2008, would take place on 18 February.[100]

A general election was held in Pakistan, according to the revised schedule, on February 18, 2008,).[101][102] Pakistan's two big and main opposition parties, the Pakistan Peoples Party (PPPP) and the Pakistan Muslim League (N) (PML (N)), won majority of seats in the election and formed a government. Although, the Pakistan Muslim League (Q) (PML (Q)) actually was second in the popular vote, the PPP and PML (N) have formed the new coalition-government.

On August 7, the deadlock between ruling parties ended when the coalition government of Pakistan decided to move for the impeachment of the President before heading for the restoration of the deposed judiciary. Moreover, they decided that Parvez Musharraf should face charges of weakening Pakistan's federal structure, violating its constitution and creating economic impasse.[103]

After that, President Parvez Musharraf began consultations with his allies, and with his legal team, on the implications of the impeachment; he said that he was ready to reply to the charges levied upon him and seek the vote of confidence from the senate and the parliament, as required by the coalition parties.

However, on August 18, 2008, President Parvez Musharraf announced in a televised address to the nation that he had decided to resign after nine years in power