[3] In 2021, Ismail Khan returned to arms to help defend Herat from the Taliban's offensive, which he and the Afghan Army lost.

In early March of that year, there was a protest in front of the Communist governor's palace against the arrests and assassinations being carried out in the countryside by the Khalq government.

The government led by Nur Mohammed Taraki responded, pulverizing the city using Soviet supplied bombers and killing up to 24,000 citizens in less than a week.

[12] As Emir of Herat, Ismail Khan exercised great autonomy, providing social welfare for Heratis, expanding his power into neighbouring provinces, and maintaining direct international contacts.

[13] Although hated by the educated in Herat and often accused of human rights abuses, Ismail Khan's regime provided security, paid government employees, and made investments in public services.

[14] However, during his tenure as governor, Ismail Khan was accused of ruling his province like a private fiefdom, leading to increasing tensions with the Afghan Transitional Administration.

Ismail Khan was ultimately removed from power in March 2004 due to pressure by neighbouring warlords and the central Afghan government.

Ismail Khan's forces even fought skirmishes with the Afghan National Army, in which his son, Mirwais Sadiq was killed.

Because Ismail Khan was contained by the Afghan National Army, the warlords who opposed him were quickly able to occupy strategic locations unopposed.

Ismail Khan was forced to give up his governorship and to go to Kabul, where he served in Hamid Karzai's cabinet as the Minister of Energy.

[18] Guantanamo captive Abdul Razzaq Hekmati requested Ismail Khan's testimony, when he was called before a Combatant Status Review Tribunal.

Carlotta Gall and Andy Worthington interviewed Ismail Khan for a new The New York Times article after Hekmati died of cancer in Guantanamo.

In July 2021, Ismail Khan mobilized hundreds of his loyalists in Herat in support of the Afghan Armed Forces to defend the city from an offensive by the Taliban.

[10] Following news of his dismissal, rioting broke out in the streets of Herat, and President Karzai had to ask him to make a personal appeal for calm.