The new indictment against Terry Peace, Cory Robert Williamson and Brian Edward Cannon contains one additional count of conspiracy to use weapons of mass destruction, which is a terrorism charge.
Federal Magistrate Walter Johnson stated during the proceedings that he was confused as to why the new charge was just now being brought with the case was ruled ready for trial.
The Federal prosecutor said that the count had to be approved by the National Security Office in Washington D.C. and that process took a long time.
After the pleas were entered, Judge Johnson set a deadline of January 20th for additional motions to be filed in the case.
Federal agents have said in arrest warrants that Peace, Williamson and Cannon illegally attempted to obtain firearms and explosives and were plotting to sabotage power transfer stations and water treatment facilities.
The three men have been in jail since their arrest in February.