Throughout the 1990s, Mehsud studied on and off at madrasas Jamia Imdadia, Jamia Haleemia and Jamia Farooq-e-Azam in Faisalabad, Jamia Nusratul Uloom in Gujranwala, and Jamia Ahsan-ul-Uloom and Jamia Yaseenul Quran in Karachi. Around 1996-1997, Mehsud's religious education was interrupted as he left to Afghanistan to fight alongside the Taliban and allied jihadist forces against Ahmad Shah Massoud's Northern Alliance. He fought in various battles during the latter phase of the Afghan Civil War like the Battles of Mazar-i-Sharif and battles north of Kabul. Noor Wali Mehsud then returned to Pakistan to finish his religious education, graduating in 1999. Upon graduating, Mehsud started using the title mufti denoting his Islamic religious scholarship. Over the next two years, Mehsud taught Islamic theology at Madrassa Imdad-ul-Uloom in the Gorgoray area in South Waziristan.
Following the 2001 September 11th attacks and the subsequent United States invasion of Afghanistan, Mufti Noor Wali Mehsud returned to Afghanistan with a convoy of Deobandi Jamiat Ulema-e-Islam fighters lead by Maulana Mirajuddin Mehsud in hopes of propping up the Taliban regime. Despite the efforts of foreign jihadists, the Taliban government was overthrown by US and Northern Alliance forces in December 2001, prompting Mufti Noor Wali Mehsud to retreat across the border into Pakistan, along with droves of Afghan Taliban, Al-Qaeda, and other jihadist fighters. Over the next year, Mufti Noor Wali Mehsud, along with many other jihadists and jihadist sympathizers in the Federally Administered Tribal Areas, sheltered fleeing Taliban and Al-Qaeda fighters, providing them a launching pad for their insurgent operations in neighboring Afghanistan. Under pressure from the US, Pakistan began deploying troops throughout the FATA and along the border with Afghanistan with the goal of apprehending jihadists seeking shelter in Pakistan. This move was considered an unprecedented violation of the tribes's sovereignty and was condemned by many parties across Pakistan. Throughout 2002-2003, Pakistan began to intensify their military presence and began launching counter-terrorism operations within the FATA, only to be met by more condemnation and suspicion by various local tribes and political parties. In addition, the localPashtun tribes began to feel that they were being subjugated by the Pakistani military. Not only was their military presence a violation of their sovereignty, but according to Mufti Noor Wali Mehsud, Pakistan's demand for the release of the jihadists whom they sheltered would be a violation of the principle of Melmastia, a major component of Pashtunwali. It was in this environment, Mufti Noor Wali Mehsud saw the need for a "defensive jihad" in Pakistan to resist American imperialism. Noor Wali joined the Mehsud branch of the Pakistani Taliban in 2003, shortly before the start of the War in Northwest Pakistan.
War in Northwest Pakistan
Early insurgent activities
Fighting broke out on March 16, 2004 with the start of the Battle of Wanna, in which the Pakistani army began an operation to clear out Al-Qaeda jihadists from the Wanna area in South Waziristan, being met with fierce resistance. In this battle, Mufti Noor Wali Mehsud lead local Taliban fighters in an ambush of the Pakistani army in Tayar Manza. The Battle of Wanna ended in a Pakistani victory, but marked the beginning of the War in Northwest Pakistan. A ceasefire was signed in April 2004, but was quickly broken, as fighting in the tribal areas continued throughout 2004. During a Pakistani military operation in September 2004, Mufti Noor Wali Mehsud was put in charge of the local organization and lead the local Talibans against the Pakistani army. Due to Noor Wali's religious education, he was made a qazi in a TTP court. According to locals, Mufti Noor Wali Mehsud famously sentenced TTP leader Baitullah Mehsud to three days in jail.