The following script is from "Guantanamo" which aired on Nov. 3, 2013. The correspondent is Lesley Stahl. Rich Bonin, producer.
Brigadier General Mark Martins has one of the toughest missions there is in the war on terror -- not on the battlefield -- but in the courtroom of a special military commission. It will hold what's being called "al Qaeda's Nuremberg," the first trial of those charged with plotting the attacks on 9/11, 12 years ago. And as chief prosecutor, Martins will be asking for the death penalty.
Every six weeks for the last year and a half, Gen. Martins and his team of prosecutors, defense lawyers, bailiffs, interpreters -- about 250 people in all -- are airlifted aboard a government charter to the U.S. naval base at Guantanamo Bay, Cuba, at a cost of $90,000 a flight.
[Greeter: Hello everyone and welcome back to Guantanamo Bay, Cuba, pearl of the Antilles.]
When the trial begins more than a year from now, it'll be the biggest war crimes tribunal since Nuremberg and much of the burden rests on Gen. Martins' shoulders.
Lesley Stahl: So when it's a military tribunal or commission, how is it different from a civilian proceeding?
Gen. Martins: The similarities really swamp the differences. I mean, the accused is presumed innocent, the prosecution must prove guilt beyond a reasonable doubt.
Gen. Martins knows a lot's at stake: the 9/11 defendants must be seen as getting a fair and legitimate hearing.
Gen. Martins: We've got to ensure that what we do in these cases is justice and can't be accused of being vengeance. And that's a great challenge.
Lesley Stahl: Now we have talked to some of the defense attorneys and they've told us it's a show trial.
Gen. Martins: Uh-huh (affirm).
Lesley Stahl: It's a charade.
Gen. Martins: Well, I mean, I don't think the test of any system is what the defense counsel say about it.
But hard as he tries to ensure that it's seen as a fair trial, he keeps running into one obstacle after the next --starting with the reputation of the venue itself -- Guantanamo Bay -- where 164 detainees sit in cells, most of them for nearly 12 years. And, except for the 9/11 five, most have not been charged. One of them cried out when he saw our cameras.
Detainee: Please, we are tired. Either you leave us to die in peace, or either tell the world the truth. Let the world hear what's happening.
Lesley Stahl: Twelve years. With no charges.
Gen. Martins: That's one of the reasons I have a sense of urgency to try everybody that we can try.
Lesley Stahl: Does it in any way taint what you're doing?
Gen. Martins: I wouldn't characterize it as taint. I believe that it influences people's perceptions.
Another thing that influences perceptions is the elephant in the courtroom: the question of torture. All five of the 9/11 defendants were held incommunicado for years at CIA black sites, where they were subjected to harsh interrogation techniques. They were legal at the time, but have since been banned by the Obama administration.
Walid bin Attash's attorney, Cheryl Bormann, says she's not allowed to talk about the interrogations because they've been classified.
Lesley Stahl: Was your client waterboarded?
Cheryl Bormann: I can't answer the question. A proposed protective order bans me from telling you anything I know about what happened to my client, beginning from the moment of his capture in 2003 until the moment that he landed in Guantanamo Bay in 2006.
Lesley Stahl: So if you were to tell me that he was subjected to a specific, harsh interrogation technique, you would be breaking a law? You would be--
Cheryl Bormann: I would be.
Lesley Stahl: --convicted of something?
Cheryl Bormann: I would be prosecuted. And imprisoned for, I believe, up to 30 years.
David Nevin: This is not a system that is set up to deliver justice.
David Nevin represents Khalid Sheikh Mohammed - KSM, known as the architect of 9/11. Considering that KSM has admitted to the worse terrorist attack on U.S. soil, you would think the case might be open and shut. But part of the problem is that he was waterboarded 183 times in one month. Nevin filed this declaration detailing the treatment of his client. But after the censors got through with it, this is all that made it into the public record.
David Nevin: Think about this for a minute. The government says they can't talk publicly about what happened to them because it's classified. If the government didn't want to reveal its secrets to them, it shouldn't have tortured them. And yet--
Lesley Stahl: Well, no, no. The government said, "We were trying to stop the next terrorist attack." They were trying to stop the next attack. They're not all totally evil, right?
Cheryl Bormann: Good intentions-- of course not. Good intentions pave the road to hell, though. Right?
What about statements KSM made during the waterboarding? The law says any evidence "obtained" through harsh interrogation techniques is inadmissible. But there's a loophole.
Gen. Martins: It is possible for a voluntary statement to be made after a passage of time at-- in a different location perhaps with different questioners.And so, once the CIA's harsh interrogations of the five 9/11 defendants stopped, the FBI sent in a so-called "clean team" to question them all over again - but without coercion. And those statements are admissible.
Cheryl Bormann: It's like Alice going down the rabbit hole, right? You torture him for three years. You keep him in captivity after you stop torturing him in a place like Guantanamo Bay. And then you send in agents from the same government that tortured him for three years to take statements. And then if you're Gen. Martins, you say, "Well, those are now clean." Guess what? They're not.
Gen. Martins: I understand, I understand the argument. The people do not forfeit their chance for accountability because someone may have crossed a line or have coerced or subjected to harsh measures somebody who is in custody.
Lesley Stahl: So you're saying that it's unfair to the justice system not to be able to question these guys later.
Gen. Martins: The point that I reject and that the law rejects is that there can be no voluntary statements following an instance of coercion. Justice requires that you look deeper, that you determine if the statement-- even though there had been a prior instance-- was nevertheless voluntary. And there can be such statements.
Navy Commander Walter Ruiz is a military attorney representing Mustafa al-Hawsawi.
Cmdr. Walter Ruiz: Gen. Martins - I respect him. I believe he is a patriot. I believe that if our government asked him to sell ice to Eskimos he would try his best, if he believed it was in our nation's interest. But ultimately, you have a system where we've classified evidence of war crimes, where you have loopholes for torture and coercion. Every day we listen to the national anthem in Guantanamo Bay, Cuba, but yet the constitution has been kicked down the road and is persona non grata in Guantanamo Bay, Cuba.
David Nevin: At the end of the day I think we all have to look at each other and say, "Are we doing this?"
Lesley Stahl: Your client KSM, he admits that he was the mastermind of 9/11. He didn't wear a military uniform. He wasn't on a real, traditional battlefield. He hid among civilians. This is a bad guy, by his own confession.
David Nevin: Yeah, you know Lesley--
Lesley Stahl: You're not saying -- he's not the mastermind?
David Nevin: Here's what I'm saying. I'm saying that in the United States, we have a process. We follow it. We've always followed it. We apply it to everyone except not now.
There will be a lot of firsts in this trial by military commission - given the CIA's tactics, the unique nature of the crime, and unprecedented legal questions that are now being fought over in pre-trial motions at this high-security legal complex.
This is the first time cameras were allowed to videotape where the trial will take place.
Lesley Stahl: This is the courtroom where the first American war crimes trial is taking place since World War II. These tables are for the defendants. One each for the 9/11 five. And this is for Khalid Sheikh Mohammed, the self-confessed mastermind of 9/11. He's defendant number one, as you can clearly see. And this is where he sits. He has his own screen to read court documents. If he wants to hear the Arabic translation, it comes out through that box. While we were here, he appeared in court in a long henna-dyed red beard and a military camouflage jacket over a long white robe. He sat here quietly and calmly. If he had acted up, he could have been shackled.
When court is in session, the defendants are transported from a secret facility on the base, known as Camp 7, to these holding cells where they stay until they're escorted to the courtroom. They're on the so-called "black mile corridor" beneath dark sniper meshing that camouflages the walkway.
This is Khalid Sheikh Mohammed's holding cell, an 8x12-foot steel, air-conditioned room with an arrow pointing toward Mecca for when he prays.
The defendants are under constant surveillance - even, their lawyers claim... when they're not supposed to be. Another complication.
Cheryl Bormann: I'm meeting with my client in a room. And up on the ceiling, like you would normally find in a jail with a client, there's a smoke detector. And one day I'm sitting in there and my client stops one of the correctional guards and says, "That's-- what is that? You're listening, aren't you?" And-- and the guard says, "Of course we're not listening. That's a smoke detector."
She believed the guard, but decided to look up the manufacturer of the smoke detector - on Google.
Cheryl Bormann: And it turns out that they only make listening devices that are intended to look like smoke detectors and other surreptitious listening devices. We find this out while we're in Guantanamo. I go, "What?"
Motions were filed, witnesses were called and while it was confirmed that the smoke detector actually was a listening device, the judge determined that Gen. Martins and his team were not eavesdropping. But the defense lawyers suspect it was the CIA and they base that on something that happened this past January.
David Nevin: I was speaking one day in the courtroom and making innocuous, unclassified remarks and suddenly the red hockey light goes off.
When the red hockey light went off, everything stopped. That's only supposed to happen when classified information is disclosed and the only ones authorized to activate the light are the judge or the court's security officer.
David Nevin: I looked at the judge and I looked at his court security officer. And both of them looked at each other as if to say, "I didn't do it. Did you?"
Lesley Stahl: So who did it?
Gen. Martins: I don't know.
Lesley Stahl: You actually don't know to this day who did it? Were you horrified?
Gen. Martins: I don't get horrified or not. I stay in that band between grim determination and tempered optimism.
The judge found out who did it: the CIA.
Lesley Stahl: Wait a minute, are they in the courtroom?
David Nevin: No, they're not in the courtroom.
Lesley Stahl: Where are they?
David Nevin: I don't know. I'd like to know.
Lesley Stahl: So wait, they're--
David Nevin: I've demanded to know. But the government won't tell me.
Lesley Stahl: Do you think that the CIA has any kind of right to keep listening because these were terrorists or they're charging that they were terrorists. They believe that these guys were bad guys, who did a dastardly deed.
David Nevin: The constitution guarantees everybody certain rights. And one of them is that you don't listen in on the lawyers in a serious capital case. You just don't do it.
Lesley Stahl: The defense teams say that the CIA has a completely different agenda from yours.
Gen. Martins: We are going to do these trials fairly. All these allegations they can raise and we have a process to sort that out.
Lesley Stahl: I've heard people say, "Look, he's trying KSM. Why are we contorting ourselves?" These guys slaughtered 3,000 innocent people. This was not the battlefield; these were people going to work.
Gen. Martins: Well, I understand the point of the view and the criticism. The law requires, and justice requires, the prosecution must present proof beyond a reasonable double before we hold someone guilty. And we aim to dispense justice that we can be proud of.