WASHINGTON — One day in 2011, the top prosecutor in the system of military commissions set up after the Sept. 11, 2001, attacks to prosecute terrorists traveled to New York for a special meeting with Justice Department officials. A Somali terrorist, Ahmed Abdulkadir Warsame, was being held aboard an American warship after being captured in international waters off Yemen, and the official, John F. Murphy, wanted him tried at Guantánamo Bay before a military commission.



In an early test of President Barack Obama’s belief that international terrorists could be successfully prosecuted in the criminal courts, Mr. Murphy was overruled. Mr. Warsame was prosecuted in federal court in Manhattan, and after pleading guilty to providing material support to the Shabab and Al Qaeda in Yemen and to other charges, he became one of the nation’s most important terrorism informants.

To Justice Department and F.B.I. officials, their success in prosecuting Mr. Warsame and eliciting important information from him was proof that an alternative legal system was not needed to keep America safe from terrorism. But that belief — a founding principle of Mr. Obama’s national security strategy — is about to be challenged by his successor, President Trump.

Senator Jeff Sessions of Alabama, Mr. Trump’s nominee for attorney general, has long believed that the Obama administration sacrificed valuable intelligence by bringing terrorism cases in federal court. Along with other Republicans in Congress, he has argued that the isolated military prison at Guantánamo is where such terrorists should be sent and tried.