Robert S. Mueller III was awakened at home close to 1:30 a.m. on April 19 as one suspect in the Boston Marathon bombing was in cardiac arrest and the other was on the run. By 3 a.m., after an F.B.I. agent had used a fingerprint scanner on the dying suspect, Tamerlan Tsarnaev, in a hospital emergency room to learn his identity, Mr. Mueller, the F.B.I. director, had arrived in a suit and tie at his agency’s headquarters in downtown Washington. His agents gave him the bad news: two years earlier, the F.B.I. had interviewed, and closed its file on, Mr. Tsarnaev. Mr. Mueller took it in withou...