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Two decades of war in Afghanistan have helped transform the spy agency into a paramilitary organization: It carries out hundreds of drone strikes in Afghanistan and Pakistan, trains Afghan commando units and maintains a large presence of C.I.A. officers in a string of bases along the border with Pakistan. At one point during President Barack Obama’s first term, the agency had several hundred officers in Afghanistan, its largest surge of personnel to a country since the Vietnam War.

These operations have come at a cost. Night raids by C.I.A.-trained Afghan units left a trail of abuse that increased support for the Taliban in parts of the country. Occasional errant drone strikes in Pakistan killed civilians and increased pressure on the government in Islamabad to dial back its quiet support for C.I.A. operations.

Douglas London, a former head of C.I.A. counterterrorism operations for Afghanistan and Pakistan, said that the agency was likely to rely on a “stay behind” network of informants in Afghanistan who would collect intelligence on the Taliban, Al Qaeda, the stability of the central government and other topics. But without a large C.I.A. presence in the country, he said, vetting the intelligence would be a challenge.

“When you’re dealing offshore, you’re dealing with middlemen,” said Mr. London, who will soon publish a book, “The Recruiter,” about his C.I.A. experience. “It’s kind of like playing telephone.”