Judge in Sept. 11 Case Visits Former C.I.A. Black Site

In a first, a military judge at Guantánamo Bay on Friday crossed into the security zone containing the wartime prison and inspected a former C.I.A. “black site” facility at the center of a dispute over the taint of torture in the Sept. 11, 2001, case.

It was a noteworthy moment in the arc of the two-decade history of the Guantánamo trials. No war court judge had before made the five-mile trip to look at the detention operations, where the military maintains the only known, still-intact remnant of the network of overseas prisons that the C.I.A. operated from 2002 to 2009.

But Col. Matthew N. McCall, the judge, is edging toward a decision on whether the accused mastermind of the attacks, Khalid Shaikh Mohammed, and three co-defendants voluntarily confessed to conspiring in the attacks in their fourth year of detention, under questioning by F.B.I. agents at Guantánamo prison.

And the prison site he visited, called Camp Echo, has played a central but covert role in the case. From 2003 to 2004, the C.I.A. kept five prized prisoners there, near the prison facilities but out of reach of the International Red Cross. It was part of its secret overseas network that hid about 120 “high-value detainees” in such far-flung sites as Afghanistan, Thailand and Poland.

In April 2004, the agency closed the black site at Guantánamo and moved those five prisoners to other secret sites, on the advice of the Justice Department, to avoid a looming U.S. Supreme Court decision later that year that granted detainees at U.S.-controlled Guantánamo Bay access to lawyers.

After President George W. Bush ordered Mr. Mohammed and 13 other C.I.A. prisoners be moved to Guantánamo in September 2006 to face trial, federal agents used the same portion of Camp Echo