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.