Almost everything about SEAL Team 6, a classified Special Operations unit, is shrouded in secrecy — the Pentagon does not even publicly acknowledge that name — though some of its exploits have emerged in largely admiring accounts in recent years. But an examination of Team 6’s evolution, drawn from dozens of interviews with current and former team members, other military officials and reviews of government documents, reveals a far more complex, provocative tale.

While fighting grinding wars of attrition in Afghanistan and Iraq, Team 6 performed missions elsewhere that blurred the traditional lines between soldier and spy. The team’s sniper unit was remade to carry out clandestine intelligence operations, and the SEALs joined Central Intelligence Agency operatives in an initiative called the Omega Program, which offered greater latitude in hunting adversaries.

Team 6 has successfully carried out thousands of dangerous raids that military leaders credit with weakening militant networks, but its activities have also spurred recurring concerns about excessive killing and civilian deaths.

Afghan villagers and a British commander accused SEALs of indiscriminately killing men in one hamlet; in 2009, team members joined C.I.A. and Afghan paramilitary forces in a raid that left a group of youths dead and inflamed tensions between Afghan and NATO officials. Even an American hostage freed in a dramatic rescue has questioned why the SEALs killed all his captors.