The Pentagon will appeal a military judge’s ruling that Defense Secretary Lloyd Austin did not have the power to throw out plea deals reached earlier this year in the long-stalled cases against the accused planners of the Sept. 11, 2001, attacks, intensifying an unusual standoff over a seminal terrorism case.

In July, prosecutors announced they had entered into pretrial plea agreements that would allow the alleged co-conspirators to plead guilty to lesser charges and avoid the death penalty.

A judge’s decision to allow plea deals in three 9/11 cases sets up confrontation with Defense Secretary Lloyd Austin, who opposes the Guantanamo court ruling.