Michael Mukasey’s confirmation as U.S. attorney general became mired in his ambiguity over whether harsh interrogation techniques like waterboarding constituted torture. In the end, the former judge was confirmed but by the narrowest margin for his post in over 50 years.

Now, with just over two months on the job, the issue of waterboarding is back on his doorstep. So far, Mukasey is handling it better than he did the Senate.

The case involves the CIA’s destruction in 2005 of videotapes made two years earlier of the harsh interrogation of two al Qaeda operatives. The ostensible reason was to protect the interrogators from retaliations and later prosecution, a hint that the agency knew it was in territory that was at least borderline illegal.

The interrogations were too much for the FBI, which withdrew its agents from the questioning. At the time of the tapes’ destruction, they were being sought by the 9/11 commission and attorneys for Bush administration detainees and were covered by a district judge’s order not to destroy evidence of the interrogations.

All of this became public only recently and immediately became the scandal of the day with Democratic-controlled committees in the House and Senate vowing full investigations.

Mukasey so far has chosen the proper and wise course. After a preliminary investigation that found enough evidence to believe a crime — obstruction of justice — may have occurred, Mukasey reached outside of Washington for a nonpolitical career prosecutor to conduct the full investigation.

He is John Dunham, deputy U.S. attorney for Connecticut, described as a very thorough, very successful prosecutor with a background in organized crime and corruption but, not that it matters, not in national security.

Mukasey rightly rejected Democrats’ calls for an independent special counsel as was appointed in the CIA leak case. This probe does not have all the potential conflicts of interest of the leak case, let alone the possible involvement of the president and vice president. For the purposes of his investigation, Dunham will have the authority of a U.S. attorney and report to Mukasey’s deputy.

That is not to diminish the broader importance of this investigation. In the immediate aftermath of 9/11 you could explain, if not excuse, brutal excesses in interrogation of people complicit in the incineration of almost 3,000 innocents. But somewhere in the war on terror, America went off course, using methods that were not consistent with our values or what the American people would tolerate. The fact that the tapes were destroyed is evidence of that.

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