The Janus Directive was a cross-over event found in the pages of Checkmate, Suicide Squad, Firestorm, Manhunter, and Captain Atom.
The story involves inter-agency warfare among the DCU’s various metahuman government agencies. Amanda Waller, head of Suicide Squad, is imprisoned and replaced with a doppelganger who sparks the hostilities after finding secret intelligence named “The Janus Directive”. This brings the Suicide Squad into open conflict with Checkmate, Project Atom, C.B.I., Force of July, and Project Peacemaker.
The Waller replacement is exposed, as is the villain behind the scenes. The cult leader Kobra used the chaos created in the various agencies to pursue his own goal of commandeering a massive space-based microwave pulse cannon that would fry all electronic systems (not to mention human nervous systems) in the Eastern United States, and unleashing Kali Yuga – the age of chaos. Waller is able to free herself, send word to the other agencies and with some massive battles the threat posed by Kobra is eliminated.
The series is notable for collectors because the Janus Directive introduced the character of Oracle, Barbra Gordon’s post-Batgirl alter-ego.
The series is a good read and it holds up today. It is certainly some of the best writing down by John Ostrander, who was also involved in the “Legends” and “Millennium” events that preceded it.