Charlie Savage’s piece in yesterday’s New York Times about the Obama administration’s preliminary attitudes toward torture, rendition, and government secrecy is thorough, sophisticated, and balanced. In other words, it has all of the qualities lacking in the recent torture stories written by his Times colleagues, Scott Shane and Mark Mazzetti.

Savage, a brilliant reporter, won the Pulitzer Prize in 2007 for the stories he wrote in the Boston Globe about the Bush administration’s multiple abuses of power. Yesterday, he noted that, within days of his inauguration, Obama had “thrilled civil liberties groups when he issued executive orders promising less secrecy, restricting C.I.A. interrogators to Army Field Manual techniques, shuttering the agency’s secret prisons, ordering the prison at Guantánamo Bay, Cuba, closed within a year and halting military commission trials.” And all of those were, indeed, extremely important steps.

But since then, some of the administration’s legal actions, and some of the testimony of its nominees for positions in the Justice Department and Central Intelligence Agency, have raised questions about the new government’s intentions.

One of the first red flags appeared when the Obama administration told an appeals court that its predecessor had correctly invoked “state secrets” to quash a lawsuit by former C.I.A. detainees, who say a Boeing subsidiary was used to fly them to places where they were tortured.

Then Elena Kagan, the nominee for solicitor general, “said that someone suspected of helping finance Al Qaeda should be subject to battlefield law — indefinite detention without a trial — even if he were captured in a place like the Philippines rather than in a physical battle zone. Ms. Kagan’s support for an elastic interpretation of the ‘battlefield’ amplified remarks that Attorney General Eric H. Holder Jr. made at his own confirmation hearing.”

Next, CIA director-designate Leon Panetta told a Senate committee that waterboarding is torture and that the administration could not bypass anti-torture statutes. But then he added that if approved techniques were “not sufficient” to compel a detainee to divulge details of an imminent attack, he would request “additional authority”—a statement suggesting that Panetta may have made the same mistake as his predecessors, who mistook the fiction of 24 on TV for reality.

In an equally balanced piece about all of this in Salon, Glenn Greenwald correctly identified the “bottom line”: “most of the key civil liberties and Constitutional questions that linger from the dark Bush/Cheney era remain unresolved thus far. Obama has not yet embraced or rejected most of them. And that is by design.”

If Savage’s piece signals that he will now become the lead torture reporter for the Times in Washington, that is splendid news for everyone who values serious journalism.

Meanwhile, over in this week’s New Yorker, the indispensable Jane Mayer details the next big decision for the Obama administration in this area: how to handle the case of Ali Saleh Kahlah al-Marri, an alleged Al Qaeda sleeper agent, who is the last “enemy combatant” being detained in the United Sates. Mari was arrested in December 2001 as a material witness in the 9/11 attacks. But just as he was about to go on trial in June 2003, George Bush ordered the military to seize him and detain him indefinitely.

“A lower court affirmed the government’s right to detain him indefinitely.” Mayer explains. “After several appeals, the case is scheduled to be heard by the Supreme Court in April. The Court’s calendar requires the Obama Administration to file a reply to the challenge by March 23rd.”

Among the many ironies of the case is the fact that the Justice Department had gathered enough evidence against Mari to send him to jail for many years, if only the Bush administration had allowed his trial to go forward. But before allowing him to be transferred to the military, the presiding judge in the case ruled that the charges against him had to be “dismissed with prejudice,” which meant that he could not be charged with the same crimes again, to protect the prisoner’s right against double jeopardy. “As a result,” Mayer writes, “if the Obama Administration decides to charge him in the criminal system now, it has to bring a different set of charges, unless Marri’s lawyers offer a deal.”

Mayer quotes Andrew McCarthy, a National Review contributor and former federal terrorism prosecutor who defended Marri’s transfer to the brig, even though the criminal-justice system seemed to be well on its way to neutralizing Marri as a public safety threat. Why was this a good idea? Because “there’s always the chance the court will release a defendant on bail.” We all remember what a big problem that was after September 11th—federal judges rushing to bail out terrorist suspects before they went on trial.

In his 2006 book, Never Again, former Attorney General John Ashcroft wrote that “Al-Marri rejected numerous offers to improve his lot by cooperating with the F.B.I. investigators and providing information. He insisted on becoming a ‘hard case.’” Mark Berman, an early member of Marri’s defense team, told Mayer that the Bush administration “really just wanted to interrogate him” in a rough manner. “No doubt about it.”

Mayer then quotes Justice John Paul Stevens dissent in the 2004 case of Rumsfeld v. Padilla. What Stevens said succinctly summarizes the central issue at the heart of all of the debates over torture, preventive detention, and “extreme rendition”:

Executive detention of subversive citizens, like detention of enemy soldiers to keep them off the battlefield, may sometimes be justified to prevent persons from launching or becoming missiles of destruction. It may not, however, be justified by the naked interest in using unlawful procedures to extract information. Incommunicado detention for months on end is such a procedure.… For if this Nation is to remain true to the ideals symbolized by its flag, it must not wield the tools of tyrants even to resist an assault by the forces of tyranny.
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Charles Kaiser is the author of The Gay Metropolis and 1968 in America. He has been media editor for Newsweek, a member of the metro staff of The New York Times, and a reporter for The Wall Street Journal, where he covered the press and book publishing. To learn more, visit charleskaiser.com.