The judge was running out of patience. It had been three months since he ordered the government to let the prisoner talk to his lawyers, and still the government was balking.

"Lest any confusion remain, this is not a suggestion or a request that (the prisoner) be permitted to consult with counsel, and it is certainly not an invitation to conduct a further 'dialogue' about whether he will be permitted to do so," the judge wrote with unmistakable tartness. "It is a ruling — a determination — that he will be permitted to do so."

The judge was Michael Mukasey, then chief judge of the federal trial court in Manhattan. The prisoner was Jose Padilla, a U.S. citizen being held incommunicado as an enemy combatant. The government lawyers Mukasey was taking to task included James Comey, then the U.S. attorney in Manhattan, and Paul Clement, then deputy solicitor general and now acting attorney general.

Now, Mukasey is President Bush's choice to replace the departed attorney general, Alberto Gonzales. His selection should be an enormous relief to anyone who cares about the Justice Department and wants to see it recover from the multiple injuries sustained during Gonzales' tenure. He has the independence, stature, intellect and experience to help rehabilitate a battered agency.

He's no lefty squish. He would not be attorney general in the Marcus administration. But if a Michael Mukasey had been attorney general for the past six years, not only would the Justice Department be in far better shape but the war on terrorism would probably be on a stronger and therefore more sustainable legal footing.

As a former federal prosecutor in Manhattan — he served under Rudy Giuliani — Mukasey understands the importance of ensuring that career Justice lawyers are, and are perceived to be, nonpartisan. As a former judge, Mukasey has hands-on experience with how the U.S. legal system is, and isn't, equipped to handle terrorism. He presided skillfully over the trial of the "blind sheik," Omar Abdel Rahman, in the 1993 World Trade Center bombing.

Civil libertarians will not always, perhaps not even often, be happy about where Mukasey strikes the balance between security and individual rights. He upheld the government's power to use "material witness" warrants to detain potential terrorists. In the Padilla case, he found that the president has the authority to seize U.S. citizens in this country and have them held indefinitely as enemy combatants, a ruling reversed on appeal.

Mukasey defended the Patriot Act in a 2004 speech, saying the law "has become the focus of a good deal of hysteria, some of it reflexive, much of it recreational." In a Wall Street Journal op-ed after Padilla's conviction last month, he appeared skeptical about allowing Guantanamo prisoners habeas corpus rights to challenge their detentions.

But unlike the administration's most extreme legal theorists, Mukasey understands that the courts and Congress are not enemies whose involvement is to be avoided at all costs. In the Padilla case, he seemed offended, correctly so, by the government's argument that his judicial role was limited to determining — without even hearing from Padilla — whether the government had "some evidence" to support its claim that Padilla should be held indefinitely. This is not a man likely to say, as former Justice official Jack Goldsmith reports of Vice President Cheney's lawyer, David Addington, "We're one bomb away from getting rid of that obnoxious (Foreign Intelligence Surveillance) court."

I ought to disclose that Mukasey was once, briefly, my lawyer. It was 1981, and Mukasey was a partner at a New York firm representing the Wall Street Journal in an odd and ultimately unsuccessful lawsuit by a company that claimed the paper was trying to drive it out of business. I was a first-year law student, but as a summer intern at the Journal three years earlier, I had written a story of perhaps six paragraphs about the company.

So when Mukasey called to ask if I would come to New York to have my deposition taken, I was delighted to skip my civil procedure class to see some civil procedure in action. I most remember his kindness to a minor witness: Knowing of my interest in journalism, he booked a room for me at the Algonquin Hotel of literary fame.

Years later, I had occasion to call Mukasey's chambers to request that some documents be released. To my surprise, the judge himself came on the phone, asking if I happened to remember him. It was more surprising, of course, that he would remember me.

We had a nice chat. Then the judge made it clear: The papers I wanted would stay under seal.

Ruth Marcus is a member of The Washington Post's editorial page staff.