(CBS) "I could smell that I was looking at what I thought was a cover-up," says retired Army Col. Lawrence Wilkerson.
Back in Washington, Wilkerson smelled trouble, and so did his boss. Wilkerson was chief of staff to Secretary of State Colin Powell. In 2004, during the Abu Ghraib abuse scandal in Iraq, Powell asked Wilkerson to investigate how Americans had come to torture.
"I was developing the picture as to how this all got started in the first place, and that alarmed me as much as the abuse itself because it looked like authorization for this abuse went to the very top of the United States government," says Wilkerson.
In 2002, the "top of the government" was divided over whether the Geneva Convention applied to prisoners in Afghanistan. The resulting presidential directive tried to have it both ways ordering that the "Öarmed forces shall continue to treat detainees humanely" but Geneva would apply only "to the extent appropriate and consistent with military necessity...."
Itís Wilkersonís opinion that the Army chose to ignore Geneva when it issued new rules for interrogations in Afghanistan and Iraq.
"That essentially says to the troops at the bottom of the rung that you have a new game," Wilkerson says. "You can use the methods that arenít in accordance with Geneva. You can use methods that are other than when youíve been taught, trained and told you could use. That, that is an invitation, a license to go beyond that, especially when youíre also putting on them tremendous pressure to produce intelligence."
Capt. Beiring acknowledges that there was some confusion. "Because a lot of people didnít really know, what are their status? Who are these people? Did they sign the Geneva Convention? Who are they and what do we do with them? So there was some confusion," he says.
"Can you tell me whether anyone up the chain of command above you was aware that the prisoners were being shackled with their hands up about shoulder high?" Pelley asked.
"Absolutely," Beiring said.
"Who knew?" Pelley asked.
"Several of my leaders knew because we had them like that, you know, there was probably one or two like that any given day. And we didnít change the procedure if someone came through whether they were a colonel or a general, we left them the same. They seen (sic) what was going on there," Beiring answered.
Pelley asked Brand if other leaders knew what was going on.
Gen. Daniel McNeill, the top officer in Afghanistan, said ďwe are not chaining people to the ceilings.Ē
Brand disagreed. "Well, heís lying obviously. I mean because we were doing it on a daily basis," he says.
"Gen. Theodore Nicholas, he was the top military intelligence officer in Afghanistan said that he did not recall prisoners being shackled with their arms overhead. Is that reasonable?" Pelley asked.
"No," Brand replied.
"Lt. Col. Ronald Stallings told investigators, quote, 'he had no idea,' end quote, that prisoners were being chained overhead for 24 hours and more. What you seem to be saying is that it was common knowledge," Pelley said.
"Yes," Brand said.
"It wasnít being kept a secret from the chain of command?" Pelley asked.
"No," Brand replied.
We donít know whether Gen. McNeill toured the prison, Brand doesnít specifically remember him there. But Gen. Nicholas and Lt. Col. Stallings were there. 60 Minutes wanted to speak with all three, but they declined.
There were inspection tours at the prison, run by the Red Cross. But the Red Cross didnít see everything. For example, it didnít see the instructions written on a dry erase board that told the guards how long prisoners were to be chained.
"We didnít want them to know ó we didnít think they had an operational reason to know," says Capt. Beiring. "It also had other things on there like if a detainee was fighting or being punished for doing stuff wrong or if he didnít eat his food or he wasnít drinking, but yes, we erased that board so the ICRC we didnít think they had the need to know."
There was a lot the Red Cross didnít know. Medical experts say that Dilawarís injuries were so severe that, if he had lived, both his legs would have required amputation. Even worse, one soldier testified that most of the interrogators thought Dilawar had been arrested only because he was in the wrong place at the wrong time. They had come to believe he was just a cab driver.