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

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.

The Pentagon pledged in a Nov. 8 letter to victims’ families that it would fight to delay the guilty plea hearings. The announcement followed a months-long back-and-forth between the DoD, the Office of Military Commissions (OMC) and attorneys for Khalid ...