Since the US War on “Terror” started in September 2001, the media and politicians around the world have focused more on Pakistan’s Inter-Service Intelligence (ISI) than on Mushareff himself. Pressure has been mounting on Islamabad to arrest the growth of militancy inside its borders. As a result, President Musharraf has reshuffled officers holding key positions in the organization and has ordered policy changes.

Over the last 25 years, the power of the ISI has grown so great that it has been called “a state within a state” and “a rogue agency.” Former Pakistani High Commissioner in the UK, Wajid Shamsul Hasan, said, “Pakistan’s foreign policy has been run by the ISI rather than the foreign office.” Prime Ministers ZA Bhutto in the mid-1970s and Benazir Bhutto in the early 1980s tried to empower the government to conduct domestic and foreign policy independent of the ISI. Both failed dramatically.

“The ISI is an extension of the armed forces,” says former ISI Chief Lieutenant General Javed Ashraf Qazi. The agency is directed and staffed by military officers.

During the Cold War, the US appropriated funds for Pakistan to assist the Afghan rebels in combating the Soviets. The CIA had cultivated close ties with the ISI, but it failed to maintain the relationship once the Cold War was over, and the two intelligence agencies drifted apart. The ISI used their American resources to finance and arm the Taliban and send weapons to Al Qaeda training camps in Afghanistan. Meanwhile, thousands of Pakistanis joined the Taliban army. In the late 1990s, the US reportedly outfitted a Pakistani commando unit to capture Al Qaeda leader Osama Bin Laden, but, in the words of a former CIA official, “the ISI never intended to go after Bin Laden. We got completely snookered.”

Why was Pakistan so keen to support the Taliban? Driven by the ISI, Islamabad has been vying to become the dominant power in the region. To achieve that goal, a key tactic in its overall strategy has been to make Afghanistan its western satellite through support of the Taliban and Al Qaeda. By extending the parameters of its influence and training extremists in the militant camps that dot the two countries, Pakistan hoped to achieve its supreme objective - sabotaging its powerful neighbor to the east, India.

The Harakat-ul-Mujahideen (HuM), which is closely linked to Al Qaeda, is a large anti-American organization that oversees the training of militants in Pakistani and Afghan camps. Its main objective is to wrest Indian Kashmir from the state of India and place it in Islamabad’s jurisdiction. Based in Pakistan, its tactics include infiltration, bombings, and hijacking, as well as kidnapping and killing civilians. Reported links between the ISI and the Harakat precipitated the US’s warning that Pakistan could be designated a state sponsor of terrorism.

According to Peter Bergen, author of Holy War, Inc., “Western diplomats in Pakistan always said that the government … gave these groups military support and … intelligence.” He said the Kargil operation in 1999 was proof of the charge. It “was an insurgency into Indian-held Kashmir, … a joint operation by the Pakistani army and these militant groups.” Musharraf, who was Chief of Army Staff during the Kargil conflict, fueled the escalation of hostilities by sending Afghan-trained insurgents into the area while asserting that Islamabad knew nothing of their activities.

After the destruction of the World Trade Center in New York City on September 11, 2001, Musharraf was forced to demonstrate that Pakistan sided with the US and the international coalition in the War on Terror. “The ISI will have to be altered and historical baggage will have to be dumped,” he said.