“It’s been a long time coming, and I do think it’s in the right place because it was an act of war,” she said.

As he reboots the case, General Martins is also trying to rebrand the system by emphasizing changes that Congress made in 2009 — notably, a higher bar to “hearsay” evidence and a prohibition against using statements made during cruel or degrading treatment. Obama administration officials echo those arguments, saying that the current tribunals are fair, unlike those during the Bush administration.

Military lawyers for the Sept. 11 defendants say that the improvements are exaggerated and that they intend to test the claims of fairness. They are starting by asking the judge, Col. James L. Pohl, to send the capital charges back to the Pentagon for reconsideration because of problems that, they say, have crippled their ability to provide a meaningful defense. The effort could further delay the case — the arraignment is just the first step, and no trial date has been set — or create grounds for appeal.

“Mark Martins gives press conferences talking about how these men have been assigned experienced, qualified attorneys who have a background in death penalty defense, but what he doesn’t get into is all the obstacles and inadequate resources and interference with our defense,” said Cmdr. Walter Ruiz, a Navy lawyer representing another Sept. 11 defendant, Mustafa al-Hawsawi .

A defense motion notes that late in the Bush administration, the Pentagon official in charge of the commissions system decided to dismiss capital charges against a sixth suspect in the Sept. 11 plot because, she said, military interrogators had tortured him. (The remaining defendants were subjected to severe treatment by Central Intelligence Agency interrogators — Mr. Mohammed, for example, was repeatedly subjected to the suffocation technique called waterboarding — although their lawyers are prohibited from speaking publicly about that.)

But the defense lawyers said they were hindered from making the case that execution should be removed at the outset as a potential penalty for their clients, too. They cited delays in obtaining approvals and security clearances for interpreters and other specialists, a prison security policy of looking through privileged attorney-client material, and disputes over access to information.

General Martins said the government took seriously its need to ensure an adequate legal defense. He characterized such complaints as positive because they demonstrated that the defendants were being represented zealously.

Photo

“I think it’s healthy,” he said. “We have an adversarial system. If I were the defense counsel, I’d never be fully happy with the resources the government gave me. But I think we’ve addressed it.”

Advertisement Continue reading the main story

A Rhodes Scholar who graduated first in his class at West Point , General Martins served as an infantry officer before attending Harvard Law School. He was a year ahead of President Obama , and worked alongside him on the law review.

General Martins became a uniformed lawyer. Mr. Obama eventually became a senator. Aspiring to the Democratic presidential nomination, he criticized the Bush administration’s original tribunals, which the Supreme Court struck down because Congress had not authorized them, and he voted against the Military Commissions Act of 2006, which revived them.

Newsletter Sign Up Continue reading the main story Please verify you're not a robot by clicking the box. Invalid email address. Please re-enter. You must select a newsletter to subscribe to. Sign Up You will receive emails containing news content , updates and promotions from The New York Times. You may opt-out at any time. You agree to receive occasional updates and special offers for The New York Times's products and services. Thank you for subscribing. An error has occurred. Please try again later. View all New York Times newsletters.

In January 2009, Mr. Obama shut down the tribunal cases then in progress — including a previous version of the Sept. 11 case, then in pretrial motions — and appointed a task force to review detainee policies. General Martins returned from Iraq to help lead the effort.

That May, Mr. Obama announced that detainees would be tried in civilian court whenever possible, but that he would keep commissions too — after Congress made them fairer. Lawmakers enacted a new Military Commissions Act modeled on an alternative version of the 2006 bill for which Mr. Obama had, to little notice, voted.

In November 2009, Attorney General Eric H. Holder Jr. announced that the Sept. 11 case would be prosecuted before a federal court in Manhattan . But the plans collapsed amid an uproar over security — and as critics pressed the administration to explain why, if its overhauled commissions were legitimate, it could not try all terrorism cases there.

Divided internally, the administration entered a year of indecision. Congress imposed new obstacles to prosecuting Guantánamo detainees inside the United States. Last spring, Mr. Holder grudgingly conceded that the Sept. 11 case had to be tried before a commission after all, and a grand jury indictment against the defendants in New York was unsealed and dismissed.

In an interview last December, Mr. Holder called the failure to follow through on his plan a “missed opportunity,” saying, “We would not have closed down Lower Manhattan, we’d be finished with that trial by now, and it could be something we could point to and show that we can be fair even to those we despise.”

Meanwhile, as the tribunals geared back up, the Pentagon general counsel, Jeh Johnson, asked General Martins — then leading a project to spread the rule of law in Afghan society — to take over as lead prosecutor.

Advertisement Continue reading the main story

In preparing for the Sept. 11 case, he increased efforts to strike plea deals with detainees accused of lesser crimes in exchange for voluntary testimony against more significant suspects.

He has also delivered speeches urging critics to give the tribunal system another chance, arguing that its rules are now closer to those in federal civilian court and that it comports with the rule of law. He frequently notes that Congress and the executive branch, under both parties, have reached a consensus that tribunals are appropriate for holding terrorists accountable.

Some continue to favor civilian courts, whose legitimacy is unquestioned and which have handled hundreds of terrorism cases, lowering the risk that a judgment will be overturned on appeal. This week, a man who plotted suicide bombings on the New York subway was found guilty in federal court.

Such skeptics include Donald Guter, a retired rear admiral who was the top Navy lawyer after the Sept. 11 attacks and fought the Bush administration’s push for draconian tribunals. Admiral Guter, who will attend the arraignment on behalf of Human Rights First, said he doubted that the system would “ever get credibility back” despite the improvements, but he praised General Martins.

“If you’re going to do this, he’s the right guy to be doing it,” Admiral Guter said. “But you’re still left with a system that is less than the proven federal system, and unnecessarily so.”