The 25-year-old militant commander, popularly known as Zakir Musa, was chief of Ansar Ghazwat ul Hind, an affiliate of the Islamic State in India. He was the first Kashmiri militant to pledge allegiance to Al Qaeda, which had also expanded its presence in the Indian subcontinent.

A graduate of engineering college in the Indian state of Punjab, Mr. Musa embraced militancy after what his family members had described as “humiliation” by Indian forces. He disappeared from home in the summer of 2013, leaving a note for his family not to search for him.

What made Mr. Musa dangerous in the eyes of the Indian authorities was that he took the grievances in Kashmir, long a domestic political issue, and tied them to causes championed by extremist organizations such as the Islamic State. His violent vision was in sharp contrast to traditional Kashmiri separatist leaders who have frequently sought the intervention of Western powers to resolve Kashmir disputes politically.

Residents in Tral, the village where the commander was killed, described the operation against him late on Thursday as a trap. Witnesses said security forces, pretending to be a gathering of supporters, had shouted, “Musa Musa, Zakir Musa,” a slogan popularized by teenagers in Kashmir. When the commander walked out of his three-story house, he was shot.