During the Third Afghan Civil War, the Taliban fought the Northern Alliance and took control of most of the country, establishing the First Islamic Emirate for which Omar began to serve as Supreme Leader in 1996.

While initially remaining quiet and focused on continuing his studies, Omar became increasingly discontent with what he perceived as fasād in the country, ultimately prompting him to return to fighting in the Civil War.

While ruling between 1996 and 2001, the Taliban were widely condemned for committing massacres against civilians; discrimination against religious and ethnic minorities; banning women from school and most employment; and the destruction of cultural monuments, including the Buddhas of Bamiyan, which Omar personally ordered.

Omar remains a largely popular figure amongst the Taliban, who view him as a key freedom fighter who defended Afghanistan's Islamic principles — first against the Soviet empire and later against the Western world.

[27] According to former Afghan President Hamid Karzai, "Omar's father was a local religious leader, but the family was poor and had absolutely no political links in Kandahar or Kabul.

[22] In 1983 he moved with mujahideen friends to Maywand District in Kandahar Province and fought under Faizullah Akhundzada, the commander of a group affiliated with Harakat-i-Inqilab-i-Islami (Islamic and National Revolution Movement).

[22] According to Dutch journalist Bette Dam, in research published in 2019, he went to Pakistan on one other occasion during the war, to fetch weapons following a dispute within his mujahideen group.

According to Ahmed Rashid, Omar joined the mujahideen group Hezb-i Islami Khalis and fought under the command of Nek Mohammed against Mohammad Najibullah's communist regime between 1989 and 1992.

[26] After Najibullah's government collapsed in 1992, Omar and a group of mujahideen turned their base near Haji Ibrahim Mosque in Gheshano village, in the Singesar area, into a madrassa.

[48] In early 1994, Omar led 30 men armed with 16 rifles to free two young girls who had been kidnapped and raped by a warlord, hanging him from a tank gun barrel.

Described as a "reclusive, pious and frugal" leader,[23] Omar rarely left his residence in the city of Kandahar, and he only visited Kabul twice between 1996 and 2001 during his tenure as ruler of Afghanistan.

"[54][55][56] During his tenure as Afghanistan's ruler, Omar seldom left the city of Kandahar, where he lived in a large house reportedly built for him by Osama bin Laden, the Saudi militant who was the founder of al-Qaeda.

According to Pakistani journalist Rahimullah Yusufzai, Omar stated in the late 1990s, "We have told Osama [Bin Laden] not to use Afghan soil to carry out political activities as it creates unnecessary confusion about Taliban objectives.

He asked bin Laden to stop talking about the jihad, but as a matter of Pashtun tribal custom did not outright forbid him, as it would be deeply insulting to a guest.

[66] Information and Culture Minister Qadratullah Jamal told Associated Press of a decision by 400 religious clerics from across Afghanistan declaring the Buddhist statues against the tenets of Islam.

[72] In July 2000, Taliban leader Mohammed Omar, in an effort to eradicate heroin production in Afghanistan, declared that growing poppies was un-Islamic, resulting in one of the world's most successful anti-drug campaigns.

Nonetheless, high-ranking Taliban officials attempted to persuade Omar to hand bin Laden over and made offers to the United States through its contacts with Pakistan.

[78]On the night of 7–8 October 2001, shortly after the US-led United States invasion of Afghanistan began, Omar's house in Kandahar was bombed just after he had left, fatally injuring his 10-year-old son.

[84] According to fellow Taliban fighters, Omar had secretly fled his residence in Kandahar for security purposes shortly after it was bombed and was last seen riding on the back of a motorcycle driven by his brother-in-law and right-hand man, Mullah Abdul Ghani Baradar.

In November 2001, he was heard over a short-wave radio ordering all Taliban troops to abandon Kabul and take to the mountains, noting, "defending the cities with front lines that can be targeted from the air will cause us terrible loss".

[87][88] On 28 November 2001, while under attack by a Russian-made BM-21 multiple rocket launcher, Texas 17 observed Omar's black American-made Chevrolet Suburban passing Kandahar Airport and travelling down highway four surrounded by a dozen sedans and six semi-trucks.

But according to Bette Dam, in research published in 2019, and Borhan Osman, a senior analyst at International Crisis Group (ICG), Omar spent the rest of his life living in Zabul province.

Bette Dam wrote, "Though Mullah Omar did not venture outside for fear of being caught, according to Jabbar Omari, in the four years they hid in that home, they felt relatively safe."

[38][91] After the US established Forward Operating Base Lagman a few hundred metres from the house in 2004, Omar relocated to a shack in a remote hamlet on the edge of a river, about 20 miles southeast of Qalat in Shinkay District, close to the Durand Line.

Afghanistan and Pakistan analyst Michael Semple, for example, wrote in a December 2014 report that "Mullah Omar remains the Taliban supreme leader and the source of all authority in the movement.

In it he promised "more Afghan War", and he also said that the more than one hundred suicide bomb attacks which occurred in Afghanistan in the last year had been carried out by bombers who acted on religious orders which they received from the Taliban – "the mujahedeen do not take any action without a fatwa.

However, Mujahid and Yousuf quickly denied sending the messages and they claimed that their mobile phones, websites, and e-mail accounts had all been hacked, and they swore revenge on the telephone network providers.

The man described ISIS leader Abu Bakr al-Baghdadi as a "fake caliph", and he also said that "Baghdadi just wanted to dominate what has so far been achieved by the real jihadists of Islam after three decades of jihad.

"[112] On 29 July 2015, Abdul Hassib Seddiqi, the spokesman for Afghanistan's National Directorate of Security, said "officially" that Mohammed Omar had died at a hospital in Karachi, Pakistan, in April 2013,[113] and the office of Afghan President Ashraf Ghani confirmed that information on his death was "credible".

[114] Pakistani newspaper The Express Tribune reported that a former Taliban minister and current leadership council member, who spoke anonymously, said Omar died from tuberculosis.