Chief Prosecutor Brig. Gen. Mark Martins wants to bolster support for the military commissions process, which critics say is fundamentally flawed and unfair. (Jim Watson/AFP/Getty Images)

When the biggest terrorism trial in U.S. history resumes this weekend at Guantanamo Bay, Cuba, Khalid Sheik Mohammed will retake his place at the defense table, the alpha dog among the five defendants accused of orchestrating the Sept. 11, 2001, attacks.

Across the courtroom from Mohammed, facing him for the first time, will stand the tall, one-star general the Pentagon has entrusted with not only securing a death penalty conviction but also convincing a skeptical world that a military commission can deliver a fair trial.

In 2009, the Obama administration, working with Congress, modified military commissions in an effort to offer more due process to defendants. But more than a decade after the system was originally set up under George W. Bush, much of the human rights community continues to lambaste it as a sham — one that should not supplant federal criminal trials for terrorism suspects.

Now Army Brig. Gen. Mark Martins, who will be the lead trial prosecutor in the Sept. 11 case, wants to bolster support for the modified process, and he’s in the fight of his career.

“If observers will withhold judgment for a time, the system they see will prove itself deserving of public confidence,” Martins said last month in a speech at his alma mater, Harvard Law School.

The address, which Martins delivered in full dress uniform, was the third in a series of appeals he has made to the legal community since becoming chief military prosecutor in October. Speaking in the particular language of the law and drawing on history and precedent, Martins has been urging the country’s lawyers — and by extension the larger public — to reexamine what he knows is a deeply ingrained belief that the tribunals at Guantanamo can provide only second-class justice.

The hope, proponents of reformed military commissions say, is that the public will come to see the system as one that provides defendants with the resources to mount a robust defense — including expert counsel — while barring the use of evidence tainted by torture or abuse and treating classified information in much the same way as it is handled in federal court.

“Mark understands the need for public legitimation, and he’s definitely making inroads,” said Jack Goldsmith, a law professor at Harvard who was a senior Justice Department official during the Bush administration. “He’s given [commissions] the appearance and the reality of more transparency.”

Critics of the system acknowledge that he has brought a new willingness to engage with detractors and a commitment to opening up the proceedings. They are, for instance, now screened for journalists and the public via closed-circuit television at Fort Meade in Maryland.

“He has the power to get things done, and that’s a change,” said a military defense lawyer, who spoke on the condition of anonymity to discuss a superior officer. “If he says he will do something, it gets done.”

Martins takes to a broader stage to make his case on Saturday, when Mohammed and his co-defendants will be arraigned at Guantanamo and could indicate whether they plan to defend themselves.

Attorneys for the five defendants say their preparations for trial have been “crippled” by government interference with attorney-client communications. They also complain that they have been unable to obtain some classified evidence and do not have enough Arabic translators and investigators.

“The odds continue to be silently and deliberately stacked against a fair process,” Navy Cmdr. Walter Ruiz, who represents one of the five men, Mustafa al-Hawsawi, said in a statement this week. “These men are represented on paper only, not in substance.”

Andrea Prasow, senior counterterrorism counsel at Human Rights Watch, said she worked with Martins on detention issues in Afghanistan and found him to be “really interested in hearing our comments.” And he oversaw improvements in the detention system at Bagram air base in Afghanistan, she said.

But Prasow insists that the justice system at Guantanamo is fundamentally flawed and cannot be salvaged by any one individual, no matter how well-intentioned. Federal court simply provides greater due process, she said, adding that any verdict that emerges from a military commission will never have the same legitimacy as one in a civilian criminal proceeding.

Prasow said commission proceedings could allow the admission of intelligence or information whose exact source is unknown — and whose origin the government would not have to divulge — leaving open the possibility that some of it was obtained through torture. She also said the commissions appear designed to hide the history of the CIA’s secret overseas prisons and that defendants might not be allowed to testify publicly about any mistreatment.

Martins said that, under the Military Commissions Act of 2009, prosecutors are barred from using any evidence derived from torture or cruel, inhuman or degrading treatment, and cases will be built on a host of other material.

Critics in the human rights community “perform an invaluable role of accountability,” Martins said in a recent interview, adding that they are sometimes focused on “a vision of rights” that is not attainable. “I believe there is a narrow category of cases where military commissions are the appropriate choice and the best choice.”

He said a hearing would be closed temporarily only to protect “sources and methods,” not to shield the government from any embarrassment stemming from the past actions of any agency.

“I very much see the job in the tradition of the public prosecutor — dedicated to implementing the law, not winning at all costs,” Martins said. “There is definitely a vigorous debate [about commissions], but I’m seeing people who are listening. I’m hearing people say, ‘I didn’t know that.’ ”

Last year, in the face of fierce congressional and local opposition, the Obama administration abandoned plans to move the trial of Mohammed and his alleged co-conspirators to Manhattan. Officials at the Pentagon immediately began to scout for what Goldsmith called a “game-changer” — a figure with the kind of national security and intellectual chops to engage with the civil liberties establishment.

“Mark Martins is one of the finest and smartest officers in the U.S. military,” said Jeh Johnson, general counsel at the Defense Department. “I urged his appointment because Mark was involved in the reforms we developed in 2009, and I knew he would bring the right sense of military justice and care for the credibility of the system.”

Martins, 51, grew up in the military, the son of an Army neurosurgeon who became the head of neurosurgery at Walter Reed Army Medical Center. After a year at the University of Maryland, Martins was admitted to the U.S. Military Academy at West Point, where he graduated at the top of the Class of 1983. He was awarded a Rhodes Scholarship and went to Oxford University, where he studied politics, philosophy and economics from 1983 to 1985.

After a couple of years in the infantry and study at Harvard Law School, Martins rose through the ranks.

He served as trial counsel at Fort Campbell, Ky., where he was assigned to a battalion of the 101st Airborne Division — at the time commanded by a lieutenant colonel by the name of David H. Petraeus. The two have remained close since, and Martins served with Petraeus, who is now director of the CIA, in Iraq and Afghanistan.

In a statement, Petraeus described Martins as a “true national asset” and a “once-in-a-generation officer.”

After returning to Washington, Martins served on an interagency task force created by President Obama to look at future policy and helped draft the Military Commissions Act of 2009. In August 2009, he went to Afghanistan, where he was deputy commander of a joint task force running detention operations.

“I’ve worked a lot of detention policy,” said Martins, noting that when his superiors offered him the Guantanamo position, “I could not parry the idea that I was well prepared for this.”

Martins’s role as chief prosecutor at Guantanamo will be his last military assignment. He would almost certainly have been promoted to a two-star position next year, but he said that leaving before the major trials at Guantanamo were over would be disruptive.

“To place myself beyond suspicion of self-advancing motives and to offer continuity to the prosecution team through at least the end of 2014,” he announced at Harvard, “I have recently requested . . . that I not be considered for promotion.”