Pakistan's role in the War on Terror was initiated by the September 11 attacks in the United States in 2001 on the World Trade Center and the Pentagon. These acts were a new manifestation of terrorism, which altogether changed the political psyche of the world. The problem of terrorism, which had been confined to small groups and few states, was changed to a global menace.
The Saudi born Zayn al-Abidn Muhammed Hasayn Abu Zubaydah was arrested by Pakistani officials during a series of joint U.S. and Pakistan raids during the week of March 23, 2002. During the raid the suspect was shot three times while trying to escape capture by military personnel. Zubaydah is said to be a high-ranking al-Qaeda official with the title of operations chief and in charge of running al-Qaeda training camps. On March 1, 2003, Khalid Shaikh Mohammed was arrested during CIA-led raids on the suburb of Rawalpindi, nine miles outside of the Pakistani capital of Islamabad. Mohammed at the time of his capture was the third highest ranking official in al-Qaeda and had been directly in charge of the planning for the September 11 attacks.
Amidst all this, in 2006, Pakistan was accused by NATO commanding officers of aiding and abetting the Taliban in Afghanistan; but NATO later admitted that there was no known evidence against the ISI or Pakistani government of sponsoring terrorism. However in 2007, allegations of ISI secretly making bounty payments up to CDN$ 1,900 (Pakistani rupees. 1 lakh) for each NATO personnel killed surfaced
The upswing in American military activity in Pakistan and neighboring Afghanistan corresponded with a great increase in American military aid to the Pakistan government. In the three years before the attacks of September 11, Pakistan received approximately $9 million in American military aid.
In the three years after, the number increased to $4.2 billion, making it the country with the maximum funding post 9/11. Such a huge inflow of funds has raised concerns that these funds were given without any accountability, as the end uses not being documented, and that large portions were used to suppress civilians' human rights and to purchase weapons to contain domestic problems .