The Political Era of General Pervez Musharraf (1999–2008): Coup, Reforms & Controversies

The roots of General Pervez Musharraf’s rise to power lie in the Kargil War of 1999. This conflict, secretly initiated by the Pakistani military high command under Musharraf, turned into a diplomatic and military failure. While Nawaz Sharif, then Prime Minister, sought to distance himself from the debacle by blaming the army, Musharraf and his allies shifted the narrative against Sharif, claiming he compromised Pakistan’s position by negotiating a ceasefire in Washington without consulting military leadership.

In retaliation, Nawaz Sharif decided to remove General Musharraf from his position as Chief of Army Staff while Musharraf was on an official visit to Sri Lanka. On 12 October 1999, as Musharraf’s plane approached Pakistan, orders were issued to divert it mid-air, effectively denying him entry into the country. The pilot insisted there wasn’t enough fuel to land elsewhere, leading to a standoff.

Meanwhile, key generals loyal to Musharraf, including Lt. Gen. Aziz Khan, Lt. Gen. Mahmood Ahmed, and Lt. Gen. Usmani, initiated a military takeover. The elite Triple One Brigade moved in swiftly, seizing control of the Prime Minister’s House, the state television (PTV), and communication networks. Musharraf’s plane landed safely in Karachi, and the military declared a coup. Nawaz Sharif was arrested, and the constitution was suspended.

Musharraf sought judicial cover for the takeover, but Chief Justice Saeed-uz-Zaman Siddiqui refused to validate it. However, a majority of judges accepted the Provisional Constitutional Order (PCO), legalizing the coup. Siddiqui resigned in protest.

Following the coup, Musharraf assumed the title of "Chief Executive" of Pakistan and promised reforms, including accountability and eventual democracy. In March 2000, former Prime Minister Nawaz Sharif was sentenced to life imprisonment. However, after intervention from Saudi Arabia and the United States, he was exiled along with his family to Saudi Arabia under a 10-year agreement.

In July 2001, Musharraf held a controversial referendum to legitimize his presidency, which officially gave him overwhelming support to continue as President. Despite heavy criticism over its transparency, the referendum paved the way for his continued rule.

In preparation for the 2002 general elections, Musharraf helped form a new political alliance — the Pakistan Muslim League (Q), also known as PML-Q — led by Chaudhry Shujaat Hussain and Pervez Elahi. To secure a majority, 10 dissident PPP members were persuaded to break away and form a new faction called PPP-Patriots, helping PML-Q achieve the required numbers to form government.

The 2002 general elections were held on 10 October. The results were as follows:

• PML-Q: 118 seats
• PPP: 81 seats
• MMA: 63 seats
• MQM: 17 seats
• PTI: 1 seat (Imran Khan)

With support from PPP-Patriots and independent candidates, PML-Q formed the government. Zafarullah Khan Jamali was appointed Prime Minister, while Musharraf retained the presidency and his post as Chief of Army Staff.

To institutionalize his authority, Musharraf introduced the Legal Framework Order (LFO), which gave the President sweeping powers, including the authority to dissolve the National Assembly. It also introduced structural reforms in various sectors. Under the LFO, press freedom was promoted to a degree, and PEMRA (Pakistan Electronic Media Regulatory Authority) was established to regulate private media and encourage expansion of electronic channels.

In the backdrop of regional tensions, Pakistan faced a military standoff with India in the wake of the 13 December 2001 Indian Parliament attack. India accused Lashkar-e-Taiba and Jaish-e-Mohammed of orchestrating the attack and mobilized 700,000 troops near the border. In response, Pakistan deployed 300,000 troops, and both countries stood on the brink of war for nearly 10 months until international diplomacy, especially from the US, helped de-escalate the situation.

To counter international pressure, Musharraf banned several militant organizations on 12 January 2002 and clarified Pakistan’s anti-terror position. Yet tensions remained high until the missile balance was reasserted. On 26 May 2002, Pakistan successfully tested the Ghauri missile, demonstrating long, medium, and short-range strike capabilities over three days.

During his presidency, Musharraf faced three assassination attempts:

• 14 December 2003 – A roadside bomb near Rawalpindi failed to detonate.
• 25 December 2003 – Another attack on his convoy using explosives and gunfire.
• 23 March 2004 – A planned attempt involving al-Qaeda-linked militants was foiled.

9/11 Attacks and Pakistan’s Role in the War on Terror

On September 11, 2001, a horrific terrorist attack shook the United States and the world. Commonly known as 9/11, the incident involved four hijacked commercial airplanes. Two planes crashed into the Twin Towers of the World Trade Center in New York, one struck the Pentagon in Washington D.C., and the fourth, believed to be headed towards the U.S. Capitol, crashed in Pennsylvania after passengers resisted the hijackers. Nearly 3,000 people lost their lives, and the event sparked a new era of global security concerns.

In response, U.S. President George W. Bush announced a global “War on Terror,” declaring: “You are either with us or against us.” Pakistan, under military ruler General Pervez Musharraf, found itself under direct pressure from the United States. The Bush administration contacted Musharraf with a clear message: support us or face the consequences. At that time, Pakistan was diplomatically isolated and General Musharraf’s government lacked international legitimacy. Seizing the opportunity to re-enter the global fold, Musharraf chose to align with the U.S.

Pakistan allowed the U.S. to use two major airbases—Shamsi Airbase in Balochistan and Jacobabad Airbase in Sindh—for logistical operations in the Afghanistan war. In return, Pakistan received significant economic and military aid. However, the decision also sparked internal unrest, leading to the rise of extremism, suicide bombings, and anti-state militant groups across the country.

General Musharraf defended his decision by stating that refusal to cooperate might have resulted in dire consequences for Pakistan, possibly a U.S. invasion similar to Afghanistan. Addressing the nation, he famously said: “We have to act in our national interest.” As a result, Pakistan became a frontline ally in the U.S.-led war on terror, undertaking military operations against Al-Qaeda, the Taliban, and other extremist elements.

While this alliance temporarily improved Pakistan’s global standing, it severely destabilized the country internally. Musharraf had to balance U.S. expectations with growing resistance from religious and nationalist factions within Pakistan. This pivotal decision significantly altered Pakistan’s foreign policy, security environment, and global alignment for years to come.

The Charter of Democracy (2006)

In an unprecedented move, two of Pakistan’s major political leaders—Benazir Bhutto of Pakistan People’s Party (PPP) and Nawaz Sharif of Pakistan Muslim League (PML-N)—signed the Charter of Democracy on May 14, 2006, in London. The Charter was a mutual agreement aimed at restoring civilian supremacy and ending military interference in Pakistani politics.

For decades, the two leaders had been bitter rivals. However, under General Musharraf's military regime, both leaders found common ground. They agreed not to support military takeovers or undemocratic practices in the future. One of the Charter’s key clauses was that neither party would align with the military to topple an elected government.

The Charter also called for strengthening the judiciary, repealing the controversial 17th Amendment, ensuring transparent elections, and upholding the constitution. Although initially symbolic, this agreement set the foundation for democratic cooperation post-Musharraf, especially after the 2008 elections.

Assassination of Nawab Akbar Bugti and the Balochistan Crisis

Nawab Akbar Bugti, a prominent tribal leader and former governor and chief minister of Balochistan, was killed on August 26, 2006, in a military operation conducted under General Musharraf’s orders. His death triggered widespread unrest in Balochistan and is considered a turning point in the province’s separatist movement.

The conflict began when Dr. Shazia Khalid, a lady doctor working in Sui, Balochistan, was allegedly raped by a military officer. Akbar Bugti demanded justice according to tribal customs. When the government refused to act, Bugti began to mobilize his supporters and resisted state authority. Armed clashes between Bugti’s loyalists and the army escalated over time.

Eventually, the Pakistani military launched an operation in the Kohlu Mountains to eliminate what they described as “anti-state elements.” Akbar Bugti was killed in a cave collapse during the assault. His body was buried without a public funeral, and the government did not hand over his remains to his family.

The incident sparked violent protests across Balochistan. Trains were attacked, public infrastructure was damaged, and anti-Pakistan sentiment surged in the province. Baloch nationalist movements gained momentum, and militant outfits like the Baloch Liberation Army (BLA) escalated their insurgency.

The assassination of Bugti deepened the sense of alienation among the Baloch people. They accused the state of exploiting their natural resources—especially gas from Sui—while denying them basic rights. Bugti’s death symbolized decades of broken promises and pushed Balochistan further into instability.

The Lal Masjid Operation (2007)

The Lal Masjid (Red Mosque) incident in Islamabad was one of the most controversial and critical moments during General Pervez Musharraf’s regime. In early 2007, students from Jamia Hafsa, an affiliated female madrassa, began enforcing their own version of Shariah law. They launched moral policing, kidnapped alleged prostitutes, and demanded the implementation of Islamic law in Pakistan.

The mosque’s leadership, particularly Maulana Abdul Aziz and his brother Abdul Rashid Ghazi, openly challenged the state’s authority. As the standoff escalated, the Pakistani government tried negotiating, but tensions reached a boiling point in July 2007.

On July 3, 2007, the government launched "Operation Silence" to regain control of the mosque compound. After intense fighting that lasted over a week, the military stormed the complex on July 10. Maulana Abdul Rashid Ghazi was killed, while Abdul Aziz was arrested while trying to escape disguised in a burqa.

The operation left more than 100 people dead and intensified anti-government sentiment. It triggered a wave of suicide bombings across the country and radicalized various militant groups, which later targeted security forces and state institutions in retaliation.

Benazir Bhutto, the NRO, and Her Assassination

As international pressure mounted on General Musharraf to transition towards democracy, he agreed to a power-sharing arrangement with Pakistan People’s Party (PPP) leader Benazir Bhutto. The U.S. and U.K. facilitated secret talks between Musharraf and Bhutto in London and Dubai, resulting in the signing of the National Reconciliation Ordinance (NRO) in October 2007.

The NRO granted amnesty to political leaders accused of corruption between 1986 and 1999, including Benazir Bhutto. This deal allowed her to return to Pakistan after years in self-imposed exile.

Benazir Bhutto returned to Pakistan on October 18, 2007, to a hero’s welcome. However, her convoy was targeted by a suicide attack in Karachi the same day, killing over 140 people. She survived the attack but expressed fears about her security in the following weeks.

Tragically, on December 27, 2007, during an election rally in Rawalpindi, Benazir Bhutto was assassinated. A suicide attacker shot at her and then detonated himself. Her death plunged the country into chaos. Nationwide protests erupted, especially in Sindh, where PPP supporters—known as "Jiyalas"—vented their anger by burning trains, banks, and public property.

The assassination of Benazir Bhutto marked the end of an era and left a political vacuum in Pakistan. It also severely tarnished Musharraf’s already declining popularity and raised questions about the state's failure to provide adequate security to a former prime minister.

Nawaz Sharif’s Return to Pakistan (2007–2008)

After nearly seven years in exile, Nawaz Sharif attempted to return to Pakistan in September 2007, following a Supreme Court ruling that allowed him to come back. However, upon his arrival at Islamabad Airport, he was forcibly deported to Saudi Arabia within a few hours by the Musharraf regime, violating the court’s order.

Under rising internal and international pressure—especially after Benazir Bhutto’s return and subsequent assassination—Musharraf finally allowed Nawaz Sharif to return in late November 2007. His return galvanized the opposition and set the stage for the 2008 general elections, marking the final phase of Musharraf's rule.

Judicial Crisis and Lawyers’ Movement (2007)

One of the key turning points in Musharraf’s downfall was the judicial crisis that erupted in March 2007. General Musharraf suspended Chief Justice Iftikhar Muhammad Chaudhry, accusing him of misconduct. However, it was widely perceived as an attempt to subvert the judiciary, fearing resistance to Musharraf's plans to seek re-election while still serving as army chief.

The suspension sparked nationwide protests by lawyers, civil society, and opposition parties. The Lawyers’ Movement, also known as the “Adliya Bachao Tehreek,” demanded the restoration of Chief Justice Chaudhry. This movement evolved into one of the most powerful pro-democracy campaigns in Pakistan’s history, severely damaging Musharraf’s public image.

May 12, 2007 - Karachi Massacre

On May 12, 2007, Chief Justice Iftikhar Chaudhry planned to address the Karachi Bar Association. However, the Sindh government and pro-Musharraf political forces, particularly the MQM, opposed the visit. As a result, large-scale violence erupted in the city.

Over 45 people were killed and hundreds injured in what is now known as the May 12 Karachi massacre. The roads were blocked, and media vans were attacked. Independent TV channels captured footage of armed men openly firing in the streets, yet the state failed to take action.

The incident significantly weakened Musharraf’s position, drawing national outrage and international condemnation. It underscored the growing unrest and the breakdown of law and order under his rule.

General Musharraf’s Economic and Educational Reforms

Economic Achievements and Reforms

During General Pervez Musharraf’s regime (1999–2008), Pakistan witnessed a significant economic boom. According to the 2005 Economic Survey of Pakistan, the poverty rate decreased from 34.6% in 2001 to 23.9% in 2005. Over 12 million people were lifted out of poverty during this time. The GDP growth rate remained above 7% in multiple years, and foreign exchange reserves surged to over $16 billion.

Musharraf focused on privatization and deregulation, attracting foreign investment and increasing exports. Mega industrial projects were launched, such as the Sundar Industrial Estate and M3 Industrial Zone.

Educational Advancements

Musharraf significantly increased funding for education. The budget for education rose to 4.3% of GDP, and literacy rates improved from 45% to over 53%.

He also initiated the establishment of nine world-class engineering universities in collaboration with foreign universities. Over 5,000 students were sent abroad on scholarships for PhDs, compared to only 20 before his era.

The number of public universities rose from 31 in 1999 to 49 in 2006. English was made a compulsory language from grade 1, and science & technology were emphasized to modernize Pakistan’s education system.

National Development Projects

Under Musharraf, Pakistan saw massive infrastructure development:

• Five new dams were planned and initiated.
• Seven motorways were developed or extended, including the M1, M2, and M3.
• Gas pipeline projects like the one to Southern Punjab were extended, with a 1,138 km line costing around Rs. 31 billion.

These projects not only improved connectivity but boosted economic zones and rural development across the country.

2007 Presidential Election and Musharraf’s Decline

In October 2007, Musharraf contested for the presidency while still being the Chief of Army Staff. The move was legally controversial and led to a political crisis. Despite winning the election, the Supreme Court was expected to rule against his eligibility.

To counter this, on 3 November 2007, Musharraf imposed Emergency Rule, suspended the constitution, and removed key judges, including Chief Justice Iftikhar Chaudhry. This act led to countrywide protests and deepened his political isolation.

2008 General Elections and Resignation

The 2008 General Elections were held on 18 February 2008. The results were a clear defeat for Musharraf’s party (PML-Q):

• PPP: 124 seats (majority)
• PML-N: 91 seats
• PML-Q: 54 seats
• MQM: 19 seats
• Other parties and independents shared the remaining seats.

Faced with impeachment threats from the new ruling coalition, General Pervez Musharraf announced his resignation on 18 August 2008, bringing an end to his nine-year rule.

Read More:

• Nawaz Sharif’s First Tenure (1990–1993)
• General Zia-ul-Haq’s Era (1977–1988)

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