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.

A Guantanamo Bay detention camp judge has reinstated plea deals with three Sept. 11 defendants, ruling that Defense Secretary Lloyd Austin was wrong to rescind them.

An order from Austin made public late Friday, in which he said he was revoking approval of the plea bargain and personally assuming that decision-making authority in the 9/11 case, upended the ...