The Janus Directive is a crossover storyline between the major government organizations of the DC Universe that took place in 1989. It was written by Paul Kupperberg, John Ostrander, Kim Yale, Cary Bates, and Greg Weisman, with illustrations by Steve Erwin, John K. Snyder III, Rick Hoberg, Doug Rice, and Tom Mandrake. The individual series' in the crossover were Captain Atom, Checkmate, Firestorm, Manhunter, and Suicide Squad.
The story deals with a war between the various metahuman military/intelligence agencies in the U.S.. This includes Checkmate, Force of July, Project Atom, Project Peacemaker, the Suicide Squad, and Task Force X. They are manipulated by Kobra into fighting amongst each other as a distraction while he plots to take over the world. The titular "Janus Directive" is a piece of fake intel that the separate agencies each receive, indicating that the other agencies are plotting against them. Kobra's ultimate plan is to wipe out humanity and repopulate the Earth with an ark in space.
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Amanda Waller gathers the heads of every organization under her control in Task Force X. This includes Bronze Tiger of the Suicide Squad, Harry Stein & Harvey Bullock of Checkmate, and Bridgette D'Abo of Project: Peacemaker. Waller announces she has discovered a conspiracy called the "Janus Directive," indicating that either Force of July or Project: Atom (both rivals in American intelligence) intend to wage war on Task Force X. Peacemaker is sent to capture or assassinate Doctor Megala and General Eiling at Project: Atom. The Suicide Squad are sent to capture or kill the Force of July, and steal their leader Abraham Lincoln Carlyle's Medusa Mask. Doctor Light kills Sparkler, Ravan kills Mayflower, and Carlyle dies of a heart attack while fighting Shade. The other members are defeated and the Suicide Squad takes the Medusa Mask. Peacemaker successfully abducts Megala, but Eiling escapes in the attack. It is revealed that Eiling and Megala also heard of a "Janus Directive" indicating that the other two agencies planned to attack them. Stein believes Waller has lost her mind and he sends his operatives Black Thorn, Gary Washington, and Val Vostok to capture her. They successfully infiltrate Belle Reve, but Bronze Tiger and Captain Boomerang fight them off while Waller escapes. Eiling tracks Megala down to Checkmate Headquarters and sends Major Force to attack the facility. Waller sends the rest of the Suicide Squad to destroy Checkmate HQ and assassinate Megala. They arrive to find Peacemaker locked in battle with Major Force, while the exposed secret headquarters is televised on the news. Count Vertigo and Shade take down Peacemaker while Duchess beats Major Force in a fistfight. The captured Megala is revealed to be a body double when he explodes. Harry Stein learns that the agencies are being manipulated, but his agents are captured before they can reveal the culprit is Kobra.
Checkmate HQ moves to a new base in the Rocky Mountains, since their old base was destroyed and exposed. Harry Stein makes an alliance with General Eiling. Stein explains that several high-profile leaders in the intelligence community have been acting uncharacteristically, and he believes they have been replaced by doppelgangers. This list includes Amanda Waller, Babylon, and Doctor Megala. Kobra has his Blackadder agents execute Checkmate Knights around the world. Black Thorn and John Reed are attacked in the abandoned Atom Project facility, but they're rescued when Peacemaker flies them out and blows up the building. The real Amanda Waller hires Manhunter as an outside agent she can trust. She sends him to infiltrate a corporation connected to the Janus Directive called Anaconda Industries. Manhunter learns they are planning on using a giant microwave cannon to wipe out American cities while preserving the infrastructure. The Blackadders shoot Manhunter and believe they killed him, but he manages to escape. Simon LaGrieve enlists Firestorm to assist the Suicide Squad by threatening to expose his secret identity.
Stein and Eiling determine that Waller, whoever she is, must be stopped. They put together a massive team and launch an assault on Belle Reve. There is a massive battle between Checkmate, Firestorm, the Force of July, Major Force, Peacemaker, Project Atom, and the Suicide Squad. Waller stops the battle when she tells them they are all being manipulated. It is revealed that Kobra tried to replace Waller, but she killed her doppelganger and has been posing as them to collect intel. Manhunter poses as a Kobra agent and discovers that Kobra has built a massive space station to fire his pulse cannon. Kobra calls this his "ark," and he has kidnapped enough prisoners to repopulate the Earth. President Bush puts Sarge Steel in charge of all the agencies working together to stop Kobra. The heavy-hitters including Captain Atom, Firestorm, and Major Force are sent to take the ark out of orbit. The Checkmate Knights and the Suicide Squad are then dropped into the hangar bay to secure the hostages. There is a massive final battle as Kobra attempts to fire the pulse cannon. Sarge Steel fires a nuclear missile at the ark, but Firestorm renders it inert saving everyone inside. Silent Majority is shot dead by Kobra's scientist Valland. Lady Liberty blows up the pulse cannon but dies in the explosion. Manhunter defeats Kobra in single combat, then says Waller owes him extra and he's never doing another job for her again. Everyone evacuates while Captain Atom and Firestorm obliterate the ark.
In the aftermath, President Bush reorganizes the agencies to prevent something like this happening again. Sarge Steel is put in charge of metahuman covert activities permanently, as a cabinet-level official, with the CBI still directly underneath him. General Eiling is put in charge of all military use of metahumans, with Captain Allard now overseeing the Atom Project. Task Force X is dissolved, Checkmate becomes an independent agency with Project Peacemaker now reporting to Harry Stein. Amanda Waller remains the head of the Suicide Squad, with Major Victory of the now defunct Force of July joining her team. Bush warns Waller that she is on thin ice and will be fired if she can't learn to work with the other agencies. Kobra is placed in solitary confinement inside Belle Reve. Nightshade quits government intelligence, and breaks off her romance with Captain Atom.