GUANTANAMO BAY, Cuba >> As the United States restarts its effort to prosecute — and ultimately execute — five detainees accused of conspiring in the Sept. 11 attacks, it has fallen to Brig. Gen. Mark S. Martins both to prove them guilty and to show the world that the tribunal system is now legitimate.

“We’re going to have a fair trial,” Martins, the chief prosecutor in the military commissions system, said in an interview this week. “There are a lot of people who come to this with preconceptions about unfairness, and I would just ask people to withhold judgment. The initial version of commissions was flawed, but there has been a lot of work on reforms.”

Martins has assigned himself to lead the latest attempt to prosecute Khalid Sheikh Mohammed — the architect of the terrorist attacks, which killed nearly 3,000 people — and four other detainees who are scheduled to be arraigned on war crimes charges Saturday at the naval base at Guantanamo Bay, Cuba.

The five have been arraigned at Guantanamo Bay before, in 2008, but the Obama administration shut that case down upon taking office, then tried to move it to federal court in New York, before surrendering to a political uproar.

Several family members of victims came to Guantanamo to watch the new arraignment, including Tara Henwood-Butzbaugh of New York, whose brother, John Henwood, died in the attacks. She said she wanted “to bear witness to the process,” adding that she “absolutely” had confidence that the military system was appropriate.

“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, 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 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 — 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 policy of looking through privileged attorney-client material, and disputes over access to information.

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.

“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.”

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

Martins became a uniformed lawyer. 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.

In January 2009, 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. Martins returned from Iraq to help lead the effort.

That May, 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 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 New York. 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 Guantanamo detainees inside the United States. Last spring, 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 in December, 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 Martins — then leading a project to spread the rule of law in Afghan society — to take over as lead prosecutor.

While 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 tribunals another chance, arguing that they are now closer to those in federal civilian court and that they comport 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.

Citing their unquestioned legitimacy and tested rules, some continue to favor civilian courts, a system in which a man who plotted bombings on the New York subway was found guilty this week.

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. 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 Martins.

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