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After becoming governor of Herat the first time, he was forced to flee after the Taliban took over authority in 1995. Two years later, while organising opposition to the Taliban, he was handed over to the Taliban by old adversaries. Then in March 2000 he escaped and worked as a low-profile member of the Northern Alliance.
During the Afghan Transitional Administration, Khan was military commander of western Afghanistan (until August 13, 2003 when President Hamid Karzai decreed that officials could no longer hold both military and civil posts) and remains the governor of Herat province.
He boasts a provincial army of 25,000 men.