Event Leviathan #1, the first chapter of the new DC crossover, kicks off by destroying the entire clandestine DC community.
One of the greatest Suicide Squad stories of all time is "The Janus Directive." The crossover ran in 1989 between Suicide Squad, Checkmate, Manhunter, Firestorm, and Captain Atom. Over the course of 12 chapters, it pulled in most of the clandestine superhero services in the DC universe for Amanda Waller's incredibly intricate mole hunt. In the process, the Squad, Checkmate, Peacemaker, Firestorm, Captain Atom, the Cbi (the in-universe analogue for the CIA), and Force of July all get into it with each other until Waller reveals that she's been manipulating them all to stop Kobra from taking over the world.
I bring this up because from what I've seen in Action Comics and in this preview of Event Leviathan #1, I think it might also be Brian Michael Bendis' favorite Suicide Squad story.