This article was produced in partnership with the Pulitzer Center on Crisis Reporting.

GUANTÁNAMO BAY, Cuba — When he took over this week as the judge in the military trial of the five defendants charged in the Sept. 11, 2001, attacks, Col. W. Shane Cohen inherited 23,039 pages of public and secret transcripts; a vault with secret evidence withheld from defense lawyers by prosecutors invoking a national security exception; approximately 500 substantive legal case motions, some awaiting rulings; and more legal arguments and filings in the pipeline.

He is the third person since 2012 to preside over the complex, slow-moving proceedings, which have been bogged down over how to handle what the United States did to the terrorist suspects from 2002 to 2006 in the C.I.A.’s secret network of black sites.

More than 17 years have passed since the attacks by Al Qaeda — and seven since Khalid Shaikh Mohammed, the accused mastermind of the plot, and four accused accomplices were arraigned in the case, which carries the death penalty — and Colonel Cohen could be the first judge to set a trial date.

On his first day on the bench, he described himself to lawyers in the case as a Mormon with “a very Jewish name” who felt shock but no anger over the hijackings that killed nearly 3,000 people on Sept. 11.

He referred to the Sept. 11 defendants arrayed in front of him in the cavernous courtroom on the United States military base at Guantánamo Bay as “gentlemen” and addressed civilian defense lawyers as “sir” and “ma’am,” adopting a more courteous approach than the cutting, less indulgent judge, a Marine colonel, who presided before him.

Colonel Cohen said he had two years left on his current Air Force assignment, as a circuit judge based in Virginia, and nine years until mandatory retirement, meaning he could preside over the case for some time.

“I understand the seriousness of what we’re doing here,” he said.

His first day in court on Monday was devoted to letting lawyers question him on his qualifications and for potential bias, a practice in court-martial cases. It offered a window into the style, experience and thinking of Colonel Cohen, a 48-year-old career military lawyer, whose last assignment was as chief of the Air Force’s environmental law and litigation division.

“I do not recall ever being angry about anything that happened with Sept. 11,” he said, adding that he did not know a single victim of the attacks. On that day, he said, he was taking a defense lawyer’s course at the Bolling Air Force Base in Washington, across the Potomac River from the Pentagon.

When James Harrington, a defense lawyer representing Ramzi bin al-Shibh, one of the accused plotters, asked if the colonel was aware that the C.I.A. torture of the defendants “was a big issue in this case,” the judge responded, “I understand that the parties will be arguing over whether or not your clients were tortured.”

The judge was assigned to the case June 3. Since then, he said, he had “wondered” whether the United States Constitution applies to military commissions, and was hoping prosecutors and defense lawyers would help him “make the right decision.”

Mr. Harrington replied, “Welcome to the sewer, judge.”

The last judge, Col. Keith Parrella of the Marines, was impatient and decisive during his qualifications questioning. He took over the case in September, presided for nine months then became commander of Marine Corps security forces at United States Embassies worldwide.

Colonel Cohen appeared humble by contrast, asking at times how to pronounce the names of some in the courtroom, notably Mr. bin al-Shibh.

Mr. Mohammed, the lead defendant, sat about 30 feet away from the judge. His accused accomplices sat in rows behind him, two of them having brought shawls with images of Al Aqsa Mosque in Jerusalem, demonstrating their affinity with the Palestinians.

The judge’s official biography shows he obtained his undergraduate and law degrees from the Brigham Young University. But, unprompted, he brought up his faith when he was asked about his attitude toward Israel’s conduct in the Middle East.

“I do have some relatives that are Jewish. I am not. I am a member of the Church of Jesus Christ of Latter-day Saints,” he said. “I believe that all people, men and women, should be able to worship how, where and what they may. I have no affiliations with the state of Israel, nor do I harbor any ill will toward the religion of Islam.”

When a defense lawyer pointed out that the question was not about his religious affiliation, the judge replied, “I wanted to just put that aside because I do realize it is a very Jewish name.”

He then noted that Israel “was recognized as a state” before he was born. “Whether or not that was the correct decision or not, that’s not my decision,” he said.

Colonel Cohen also said he had never been involved in a death-penalty or multiple-defendant case in his 20 years as a military lawyer. In 2003, a year he served as a defense lawyer at United States air bases in Turkey and Japan, he said, he took capital punishment defense training to become a “learned counsel,” a specialty recognized by the American Bar Association. Each Sept. 11 defendant has one, paid by the Pentagon.

A trial prosecutor, Clayton Trivett, had only one question, to which Colonel Cohen replied that he has not applied for a civilian job at the Justice or Defense Departments.

The question was important because a federal court this year invalidated about two years of pretrial rulings in the destroyer Cole trial, the other capital case at Guantánamo, because that case’s judge secretly negotiated with the Justice Department for a civilian immigration judge position while presiding in the case with a Justice Department prosecutor.

Colonel Cohen said he read that decision and took away a one-word lesson: “Disclose.”

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