It was against this background that the Taliban emerged. Former mujahidin who were disillusioned with the chaos that had followed the mujahidin victory became the nucleus of a movement that coalesced around Mullah Mohammad Omar, a former mujahid who had returned to his home village of Singesar in Qandahar province in 1992 where he became the village mullah and head of the local madrasa. The group, many of whom were madrasa students, called themselves taliban, meaning students or seekers of knowlege. Many others who became core members of the group were commanders in other predominantly Pashtun parties, and former Khalqi PDPA members. Their stated aims were to restore stability and enforce (their interpretation of) Islamic law. The Taliban's first military operation has acquired mythic status in Taliban ranks: In early 1994 the Taliban attacked the headquarters of a local commander who had been responsible for numerous rapes, murders and lootings. Similar campaigns against other warlords followed, and the Taliban soon gained a reputation for military prowess and acquired an arsenal of captured weaponry. By October 1994 the movement had attracted the support of Pakistan, which saw in the Taliban a way to secure trade routes to Central Asia and establish a government in Kabul friendly to its interests.

According to Afghanland.com sources, The Taliban's first large military operation took place in October 1994 when it seized the Pasha munitions depot and the town of Spin Boldak on the Pakistani border, held at the time by Hizb-i Islami commanders. The capture of the arms dump provided them with an enormous quantity of military materiel, including rockets, ammunition, artillery, and small arms. Two weeks later the Taliban freed a Pakistani trade convoy that was being held by commanders demanding exorbitant tolls outside Qandahar; the convoy's real objective was to examine the feasibility of constructing a rail line along the route-a priority for the government of Prime Minister Benazir Bhutto. Shortly thereafter the Taliban took control of Qandahar after the local commander, loyal to the Rabbani government, ordered his forces not to resist. In the process the Taliban captured heavy weapons and aircraft, including MiG fighters, helicopters, and tanks. The Qandahar attack was also notable for the appearance of large numbers of afghan refugee madrasa students serving as soldiers for the Taliban, most of who entered Afghanistan by bus at the newly seized Chaman/Spin Boldak crossing with the knowledge of Pakistani border officials. By December 1994 the Taliban had spread north and east to the outskirts of Kabul and west toward Herat. Burhanuddin Rabbani called the Taliban movement as the “ Doves of freedom” as Taliban marched towards Kabul demilitarizing town after town. The Taliban goal was to unify the country, establish an Islamic society and hold elections for the establishment of a new government in Kabul. The CIA was a major backer of the Taliban and also there were hints that the Taliban were actually the army of King Zahir Shah who was in exile in Italy. Pakistani traders who had long sought a secure route to send their goods to Central Asia quickly became some of the Taliban's strongest financial backers. Pakistan took this opportunity to support this movement and have a major influence on the future policies of Afghanistan. With Half of Afghanistan in their control the Taliban began to see offers from Pakistan and Al Qaeda to aid them in unifying Afghanistan under Taliban rule in return for save haven for Al Qaeda armies of Osama Bin Laden and train militants for Pakistan to be used in the conflict in Kashmir.

In January 1995 the Taliban advanced on Kabul, squeezing Hekmatyar between their forces and the forces of Defense Minister Masood. In February, Hekmatyar abandoned his position at Charasyab and left behind significant stores of weapons. Under an apparent agreement with Masood, who was preoccupied with fighting Hizb-i Wahdat, the Taliban occupied the base at Charasyab. A massive assault by Masood against Hizb-i Wahdat then drove its leader, Abdul Ali Mazari, to strike a deal with the Taliban. But after a faction of Hizb-i Wahdat joined with Masood instead, Masood launched a full-scale assault on the Taliban, driving them out of Charasyab. Combat resumed in the late summer and fall of 1995, with the Taliban defeating Masoods forces in the west and occupying Shindand and Herat by September 3. The occupation of the strategic town of Herat by the Taliban was a terrible blow to JAMIAT-E-ISLAMI forces, and cut off the land route connecting the JAMIAT-E-ISLAMI with Iran. The Taliban's innovative use of mobile warfare hinted at a Pakistani role in the capture of Heart.

In 1996 fighting shifted to the east, and the string of Taliban victories continued, culminating in September in its greatest victories to date, the seizures of Jalalabad on September 11 and Kabul itself by the end of the month, although the bulk of the United Front forces holding the city were able to withdraw to the north intact. With the fall of Kabul, the battle lines in eastern Afghanistan largely stabilized, cutting across the fertile Shamali plain. Until early 1999, Masood remained within artillery range of Kabul and repeatedly fired rockets into the city. Though he denied targeting civilians, many were killed, including more than sixty-five in a two-day attack in September 1998. Sometime after Masood's loss of Kabul, he began to obtain military assistance from Russia as well as Iran.

In the west, fighting resumed in 1997 as the Taliban attacked the predominantly Uzbek Junbish forces commanded by General Dostum. Dostum had carved out what amounted to a mini-state in northern Afghanistan comprising five provinces and administered from Mazar-i Sharif, and up to this point had appeared to be one of the strongest powers in Afghanistan. Hizb-i Wahdat also maintained a significant force in Mazar-i Sharif (which has a large Hazara population) in an uneasy alliance with Dostum. As had happened elsewhere, however, the military stalemate was broken when one of Dostum's deputies, Gen. Abdul Malik Pahlawan (generally known as "Malik"), allied with the Taliban and turned on Dostum on May 19, 1997, arresting a number of Junbish commanders and as many as 5,000 soldiers. At this point foreign fighters began to replace the Taliban fighters and slowly the amount of Pakistani, Arab and Chechen fighters increased as moderate Taliban began to defect or quit their mission and dissolve in the countrysides.

Pakistan was quick to seize the opportunity to recognize the Taliban as the government of Afghanistan, on May 25; Saudi Arabia followed on May 26 and the UAE on May 27. But the fortunes of the Taliban were suddenly reversed at the end of May as the alliance with Malik disintegrated, apparently after Taliban troops began trying to Jamiat-e-Islami disarm the local Hazara population in Mazar-i Sharif. As the Hazaras turned on them, the Taliban soon found its fighters trapped. Hundreds of Taliban soldiers were killed in the streets of Mazar, and some 3,000, most of whom were in Dostum's headquarters at Shiberghan, were taken prisoner by Malik. Nearly all of these detainees were then summarily executed. Within days, the remains of the Taliban occupation force had been driven from the city and commanders loyal to Malik had regained control of Jowzjan, Sar-i Pol, and Faryab provinces, establishing a front line with the Taliban along the Morghab river in Baghdis province. However, the Taliban were able to consolidate control over the province of Konduz, a predominantly Pashtun pocket in the north that had come under its control after the Pashtun shura switched sides.

The Taliban troops in Konduz attacked west towards Mazar-i Sharif in early September 1997, after being reinforced with men and munitions airlifted from Kabul and gaining further aid from the defection of several commanders holding positions in the area. In fighting over the next several weeks Taliban forces were again pushed back to Konduz. During its retreat, the Taliban attacked villages along the way, killing at least eighty-six civilians. In August 1998 Taliban forces opened their third assault on Mazar-i Sharif, and this time took the city decisively. They massacred at least 2,000 people, most of them Hazara civilians, after they took the city, and killed an unknown number of people in aerial bombardments.

In August 1998, the United States launched air strikes against reputed training camps near the Pakistan border. The strikes, which the U.S. justified as attacks on the headquarters of Osama bin Laden, came in the wake of the bombings of the U.S. embassies in Nairobi and Dar es-Salaam. Following these strikes, on August 20, the U.N. and most international humanitarian agencies withdrew their staff from the country. In September 1998 the Taliban took control of the predominantly Hazara town of Bamian, west of Kabul; local activists and foreign observers documented reprJamiat-e-Islamil killings in the city after the takeover. Masood remained within artillery range of Kabul and repeatedly fired rockets into the city, killing civilians, while claiming to be targeting the airport, which is on the northeastern edge of the city.

In late July 1999, at peace talks held in Tashkent, the Six Plus Two contact group issued the "Tashkent Declaration," which called on all parties to resolve the conflict through "peaceful political negotiation," and pledged "not to provide military support to any Afghan party and to prevent the use of our territories for such purposes." Almost immediately afterwards, both the Taliban and the United Front resumed fighting, with the Taliban focusing its efforts on territory held by Masood's forces north of Kabul. As it pushed north, the Taliban forced civilians from their homes and then set fire to houses and crops, and destroyed irrigation canals and wells, ostensibly to rout opposition sympathizers but effectively preventing the residents' return. In the Shamali region, men believed to be loyal to Masood were arrested or shot, and women and children either fled or were taken to Jalalabad and Kabul. Over four days in August the U.N. estimated that over 20,000 people arrived in Kabul, bringing the total to close to 40,000 in a two-week period. Thousands more fled to the Masood-held Panjshir valley. In September, Taliban fighter planes bombed Taloqan, the capital of northern Takhar province. In October the U.N. imposed sanctions on the Taliban, banning Taliban-controlled aircraft from takeoff and landing and freezing the Taliban's assets abroad.

On September 5 the Taliban captured Taloqan. Fighting in the area, combined with the effects of a severe drought, drove thousands of civilians from the area east to Faizabad and Pakistan or north to Tajikistan. As of June 2001, Masood's forces had regained territory to the north and east of Taloqan but remained well outside the city itself. His headquarters were reported to be in Khoja Bahauddin in northern Takhar province. Elsewhere, forces believed to be loyal to Ismael Khan and General Dostum were responsible for guerrilla attacks on Taliban forces in western and northern Afghanistan in April and May 2001. On September 9 2001 two Al Qaeda suicide bombers disguised as Arab reporters seeking to interview Ahmad Shah Masood with hidden bomb in a video camera and around their waists. The Bomb blast killed Ahmad Shah Masood and a couple of aids. Ahmad Shah Masood died on September 10 2001. A day later New York City and Washington DC come under attack by suicide bombers who cashed passenger planes into the world trade center buildings and Pentagon. The United States blamed Osama Bin Laden’s Al Qaeda network for the attacks and started building a coalition to oust the Al Qaeda and Taliban from Afghanistan.

In mid-2000 the Taliban split into 3 separate groups. One group became a sub army of Osama Bin Laden who began to pay the leaders of the Taliban and directly influenced the Taliban movement. This group has a Wahabi belief and is set to bring strict Islamic rule in Afghanistan. This group enforced the strict dress code while Taliban were in power, undermining women's rights, disallowing music and film. Basically they imported Saudi Arabian culture into Afghanistan in the name of Islam.

The Second group of Taliban are paid by Pakistan's Intelligence agency (ISI). This group is made up Pakistani ISI agents, Pakistani army soldiers and Punjabi and Sindi militants dressed in Afghan clothing set to destroy Afghanistan national identity, it's art and culture, and infrastructure so Afghanistan can be under the influence of Pakistan. This group is the one who destroyed the Bamian Buddhas, The Afghan TV archives, and cultural sites. This group is the force behind continuing the war between Taliban and US, because the benefactor would be the Pakistani Government via US Aid to Pakistan. Every time there are talks of peace between a mainstream Taliban leader and the Afghan government, The ISI Taliban perform an act of violence against the Afghan and US government to derail these talks. And every time these mainstream Taliban are immediately arrested or assassinated upon their announcements for peace. The August 8th 2011 shooting of the US Helicopter is the work of the Pakistani ISI backed Taliban group. Though the mainstream Taliban are afraid of voicing any opinions in fear that their location will be identified via computer use, GPS cell phones and more. The Pakistani ISI Backed Taliban freely claim any act of violence via tweeter, facebook, text messages deep within Pakistan and they are never identified or targeted.

The third group is the actual Taliban (students of Islam) who see Jihad as a pillar of their religion and fight to preserve their faith and fight foreign invaders. They are indifferent to cultural beliefs, music, and dress codes. This group fought hard to keep the Bamian Buddhas from destruction. They are for women's right to education, and are against the Wahabisim of Afghanistan and prefer the mainstream Cairo Islamic Schools.

Judging from the cash flow of these three groups. The Pakistani ISI backed Taliban are indirectly funded by the US funds to Pakistan and in essence, the US is funding their own enemies, the Second strongest group is the Wahabi Taliban funded by the oil rich kingdom of Saudi Arabia. The Third group (Islamic Students) are fighting for a cause rather than money.