Michael Mukasey was at the doctor’s office on the morning of Sept. 11, 2001. When he heard about the attack on the World Trade Center, he asked: “Is this our guys?”

The answer: “We think so.”

That opinion came not from his physician but from the U.S. marshal who headed then-Judge Mukasey’s security detail. Six years earlier, the veteran federal jurist had presided over the conspiracy trial of 10 al Qaeda terrorists. Among the defendants was “blind sheik” Omar Abdel-Rahman, arrested after the 1993 bombing of the World Trade Center, which killed seven. By 9/11 Judge Mukasey was already acutely aware of the threat to which many Americans first awoke that morning.

He had also found it necessary to take precautions considerably more intrusive than the occasional airport pat-down. When he was assigned to the terror trial in 1995, the U.S. Marshals Service advised him to accept a security detail: “I could have turned it down, but they said, ‘Well, let’s do it on a trial basis for a while.’ . . . It wound up going for 11 years.” The marshals had a room in his apartment building and accompanied the Mukaseys everywhere they went. “It’s kind of hard to have a frank personal conversation with your wife in the car,” Mr. Mukasey says. “It has a certain inhibiting effect.”

I visited Mr. Mukasey this week at his 46th-floor law office in midtown Manhattan to hear about his experiences both before 9/11 and after, including his term as attorney general for the Bush administration’s final 14 months. He’s quick to remind me that even before 9/11, the 1993 attack was not a one-off. The trial over which he presided involved “an overarching conspiracy that included everything from the killing of [Jewish Defense League founder] Meir Kahane in 1990 by El Sayyid Nosair, to the ’93—what we now know as the first World Trade Center bombing—to a plot in ’94 to blow up various landmarks around the city: the Holland and Lincoln tunnels, the George Washington Bridge, the U.N.”

Evidence in the trial included conversations recorded by a government informant who had infiltrated the terror cell. One exchange sticks in Mr. Mukasey’s mind for what is says about both the terrorists’ mindset and America’s vulnerability. The informant and one of the defendants were walking along a New York street “looking for a piece of electronics that they could use as a detonator. The [defendant] starts to talk about, ‘Look at this society—how open it is. You can get anything here. You can get these electronics, you can get’—he segues from that to Playboy magazine and pornography and the whole span of things that are available in an open society. It was a combination of awe and contempt—awe at the openness and contempt at the notion that people could do anything they wanted. . . . The bottom line is we were ripe for plucking because of all of this.”

What makes a free society ripe for plucking is not chiefly its vices but its virtues, including the protections it affords to those accused of wrongdoing. America was not on a war footing until after the mass casualties of 9/11, and neither was Judge Mukasey: “Obviously we were treating it then as a crime, which was really the only frame of reference we had. . . . At the time, I think a lot of people felt—and I was probably among them—that it proved the suitability of federal courts to handle terrorism cases.”

He ultimately changed his view, in part because al Qaeda acquired valuable intelligence from the trial over which he presided. In a conspiracy case, Mr. Mukasey explains, “the government is required to name all the unindicted co-conspirators that it knows about, and it serves a list. It was later found that that list had found its way to Khartoum within 10 days after it was served.” The Sudanese capital was then home to one of those unindicted co-conspirators, Osama bin Laden. “So bin Laden knew not only that they knew about him but also who else they knew about.”

Mr. Mukasey had other reasons to oppose the Obama administration’s plan to try Khalid Sheikh Mohammed and other top al Qaeda detainees at the New York courthouse where he once sat. “Just logistically, it would have meant shutting down Lower Manhattan for a huge period of time. . . . It would have put a target on New York City that was already there, but it would have painted it in neon.”

Even the far lower-profile 1995 trial was burdensome for members of the jury, who were kept anonymous to protect their safety: “The jurors had to be picked up every morning at a different pickup point and then dropped off in the evening by the marshals, who were careful to make sure nobody followed them. And in spite of that, we found that two of them had reporters sitting on their doorsteps the day the verdict was delivered. They were terrified.”

Perhaps most important, in the context of a wider war, civilian trials for terrorists violate Mr. Mukasey’s moral sense. “Think about the lesson: If you follow the rules of war—which is to say, you wear a uniform, you follow a recognized chain of command, you carry your arms openly, and you don’t target civilians—then you can be held until the termination of hostilities. If you violate all of those rules, we’ve got a better deal for you. We’ll give you a trial, and a platform in open court, and the possibility of an acquittal. That’s a perverse kind of logic.”

If the U.S. can hold detainees indefinitely, are trials necessary at all? Mr. Mukasey says yes: “I don’t think it’s a satisfactory resolution for anybody to have people . . . who are charged with planning 9/11 simply held indefinitely and to have the people who lost relatives and so on told, ‘Don’t worry, we’re just going to hold him indefinitely. There isn’t going to be any authoritative determination that they did what they did.’ Part of the reason we have trials is to make a moral judgment, and there are some people as to whom you have to make that judgment.”

That may happen, however belatedly. Congress has enacted legislation prohibiting the transfer of Guantanamo detainees to the U.S. In April, Attorney General Eric Holder yielded to reality and announced that KSM and four other defendants will be tried by military commissions at Guantanamo.

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Appointed to the bench by Ronald Reagan in 1987, Judge Mukasey retired in 2006. A year later, with the Senate in Democratic hands, George W. Bush tapped him to be attorney general. He commanded respect across the aisle: In 2003, Sen. Charles Schumer of New York even floated his name for the Supreme Court.

“Not having seen, and not being cleared to see, the CIA program, I was asked to pronounce that waterboarding, in the abstract . . . was torture,” Mr. Mukasey recalls. He refused. “In retrospect, I’m very glad I did that, because then I read about the program, and it didn’t violate the torture statute. . . . The torture statute defines torture as acting under color of law so as to cause severe physical or mental pain or suffering, and severe mental pain or suffering is defined in durational terms.” Waterboarding “didn’t produce physical pain . . . and there were no lasting psychological effects,” so it was permissible under the law.

By the time Mr. Mukasey took office, the question was moot anyway. He learned that the Bush administration had suspended enhanced interrogation. The Obama administration went further, barring the CIA from interrogating terrorists altogether. “The current interrogation regime is limited to the Army Field Manual,” which, Mr. Mukasey notes, “has been available on the Internet for years and is used as a training device by terrorists.”

Days after bin Laden was killed this May, Mr. Mukasey wrote in The Wall Street Journal that when Khalid Sheik Mohammed was waterboarded, he had revealed the nickname of a bin Laden courier—information that proved crucial in tracking down the al Qaeda leader. That prompted a rebuttal in another newspaper from Sen. John McCain, a Republican opponent of enhanced interrogation, who called Mr. Mukasey’s account “false.”

Mr. Mukasey tells me that Leon Panetta—then the CIA director, now the defense secretary—”wrote a very carefully worded letter appearing to agree with Sen. McCain. But if you unpack it carefully, what you’ll find is that both the statements and omissions make it very plain that information was obtained from KSM. . . . [Mr. Panetta] says, for example, that the nickname wasn’t learned from KSM; it was learned from somebody else, who was not in CIA custody. Well, yes, it was learned from a lower-level person earlier on, and it was [in] a memo that stayed in the files of the CIA for years unread, because the significance of it wasn’t apparent at the time. It wasn’t apparent until it came from KSM.”

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Two and a half years after his return to private life, Mr. Mukasey, now 70, is still very much engaged in the debate, writing and speaking often on terror policy. A vigorous critic of the Obama administration, he is not impressed when I point out that except for interrogation, Mr. Obama has ended up largely continuing his predecessor’s antiterror policies.

“Where they were coming from was articulated during the campaign, which was they felt that we had overstepped,” he says, noting that “the first thing [President Obama] did was sign an order closing Guantanamo. . . . They’ve done as much as they think they have to do, but . . . their instincts, I don’t think, are in it.”

With Americans focused on the bad economy, terror policy has so far not loomed large in the 2012 presidential campaign. Has the government’s success in preventing another 9/11-scale attack made us complacent? “I think people are less and less complacent,” Mr. Mukasey says. Smaller events like the 2009 Fort Hood massacre and the 2010 bombing attempt in Times Square have served as reminders of the threat.

“Even when we had the earthquake [on the East Coast last month], people’s immediate reaction was: Is this a terrorist act? . . . I think people remain sensitive to it, and the wound is right below the surface, and it can be opened at any moment. The Ground Zero mosque touched off some of that.” Mr. Mukasey opposes the mosque, which he describes as “a triumphalist statement.” He observes that at one point it was to be called the Cordoba House: “Cordoba was the site of a mosque commemorating a noted Muslim victory in the conquest of Spain, and was the capital of the Muslim empire in Spain.”

Mr. Obama’s support for the mosque is an example of what Mr. Mukasey calls the president’s “politically correct turn of mind.” He cites another: “Look at the paper that the president issued back in August on dealing with terrorism—’community cooperation’ or something of that sort. It’s meant to sound like harmless pap. It isn’t, really. It suggests that the thing we have to worry about most in the United States is a backlash against Muslims.”

He does have a few points of agreement with the administration. He praises the use of drone strikes against terrorists, and he thinks the appointments of Mr. Panetta at the Pentagon and Gen. David Petraeus as CIA director will enhance cooperation between the military and the intelligence community. And, of course, “the most commendable thing [Mr. Obama] did—the gutsiest thing he did—was the killing of bin Laden. He didn’t do it with a drone strike, he did it in a way that would allow exploiting whatever intelligence we could find and in a way that . . . we could be sure that we got him, and that it was him that we got.”

But that leads to a caveat: “It was a mistake to disclose that we had found a trove of information. We could have done without disclosing that, because obviously the people who dealt with [bin Laden] directly . . . I’ve got to believe that some of them changed their daily habits.” It’s reminiscent of the release of that list of co-conspirators back in the 1990s, except that this time it was an unforced error.