Aboard the USS Boxer, somewhere in the Indian Ocean, Ahmed Abdulkadir Warsame was sitting across from a team of interrogators, talking and talking. In secure meeting rooms in Washington, senior officials in the Obama administration were wringing their hands over what to do with him.

Some in the administration desperately wanted to prosecute Warsame — a key facilitator between al-Qaida franchises — in federal court. To do that, though, they needed a “clean team” of FBI agents to come in and read the Somali his rights, perhaps jeopardizing his willingness to keep talking. The quandary was particularly acute because Warsame had intelligence on Anwar al-Awlaki, a U.S. citizen and a senior leader in al-Qaida in the Arabian Peninsula (AQAP).

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