Covenant was a city in New Mexico, home to a major Cadmus facility.
After Question was apprehended by Project Cadmus, they took him to Covenant where Dr. Moon could torture him for information. After Huntress and Superman breached the security and brought back Question and Captain Atom, Amanda Waller cleaned up the location; all her supplies were moved elsewhere.
Lex Luthor had a backup plan; he hijacked the Watchtower's Binary Fusion Generator and fired it at the now abandoned complex. The blast hit the facility, but also destroyed most of the city. Most inhabitants only saw a bright light, but some saw it came from the sky. The city's buildings and infrastructure sustained heavy damage, but there were no casualties, but there were lot of people wounded.