GILGIT-BALTISTAN, Pakistan — On a clear night last month, Shams al-Haq woke to the smell of smoke and the sight of the schoolhouse near his fruit farm going up in flames.

Mr. Haq and his neighbors spent hours fighting the fire until dawn, when it became a lost cause. They soon learned that it was one of 14 schools, most of them for girls, set ablaze on the same night, over just an hour in Gilgit-Baltistan, a mountainous territory stretching across northern Pakistan.

Once again, it seemed girls’ education in Pakistan was under assault by militants.

“The extremists have shown what frightens them most — a girl with a book,” tweeted Malala Yousafzai, the Nobel laureate and education advocate who as a young student was gravely wounded by Taliban gunmen six years ago in Swat, a nearby valley.

But since then, the easy explanation has come to look like only part of the story to some who live here. And as dozens of Pakistani soldiers moved into the area after the fires, many residents began considering new theories about who — and what — might have been behind the arson spree.