Senior national security aides have tried to use an intelligence assessment — which says a complete withdrawal of American troops from Afghanistan would lead to an attack on the United States within two years — to convince Mr. Trump that a residual counterterrorism force must remain in the country.
The intelligence assessment, initially prepared in 2017 as part of Mr. Trump’s Afghanistan strategy review, was renewed late last year, according to Defense Department officials.
During internal discussions, Jim Mattis, who resigned as defense secretary last month, pointed to the estimate that some 20 terrorist groups, many of them offshoots of Al Qaeda and the Islamic State, would quickly use the freedom afforded by an American troop pullout to try to launch operations against Western targets.
Concluding that Mr. Trump does not have a grasp of the internal politics and feuding that have vexed American policymakers in Afghanistan for the past 18 years, Defense Department officials have tried to put the consequences of a full American pullout in as stark terms as possible. If the troops are withdrawn, they argue, an attack on the United States could occur in two years and Mr. Trump would shoulder the blame.
Mr. Mattis’s successor, Acting Defense Secretary Patrick M. Shanahan, told reporters on Monday that while he had been briefed on the negotiations with the Taliban, the Defense Department had not been asked yet to prepare for a complete withdrawal.
Defense officials said the Pentagon wanted to keep a counterterrorism force on the ground in Afghanistan, perhaps stationed at Bagram Air Base near Kabul. Such a force, they said, would focus primarily on conducting raids against members of some of the 20 terrorist groups on the intelligence assessment list.
The groups include the Islamic State affiliate in Afghanistan, known as Islamic State in Khorasan, and Al Qaeda. It also includes the Haqqani network, but that group is at the core of the Afghan Taliban, so it was unclear how negotiations would address that.