When it comes to having a contingency plan, or prepared backup plan, for superheroes who go bad, Batman is no stranger to formulating them, especially for someone like Superman. Compared to other superheroes, Superman is the most powerful member of the Justice League and so The Dark Knight comprehends just how dangerous an evil Superman could be when he is let loose across the DC Universe. That fear comes true in the Injustice universe in the absolute worst-case scenario.
Injustice shows audiences a glimpse at a world where Superman has created a chokehold over the planet as its leading dictator. The sequel series, Injustice 2, sees Superman in captivity, but even as a prisoner, Batman needs his contingency plans. No moment is more apropos to that truth than in Injustice 2 #5 by Tom Taylor and Daniel Sampere. In a moment where Superman is concocting a deadly escape of his own, Batman is one step ahead of him in the most unexpected way.
Batman's plan? He has The Atom shrink down to miniature size, just small enough to fit inside of Superman's head with nothing on his persons except a Kryptonite shard. The moment that Superman gets out of line, that's when Atom is instructed to stab away at Superman's brain. Granted, he's still Superman, so the blow isn't going to kill him, but at worse, it's going to give the Man of Steel a stroke or a seizure. At best, it just makes Superman collapse into an unconscious state. This may very well be the most brilliant plan that Batman ever could have come up with, at least for Superman.
Everyone knows that Batman is the World's Greatest Detective, but it's understated how that nickname also indicates Batman to be one of the most deceptively intelligent men in Gotham City. This is one of his smarter plans because it attacks the one place that Superman can't quite protect himself: from within. Externally, he's indestructible. For an alien who lets bullets ricochet off of his body with ease, there aren't many ways to harm Metropolis' former savior. However, internally, he isn't quite as indestructible. Not where his internal organs are and not when he's attacked by something (or in this case, someone) who he can't possibly see or catch.
The kryptonite is just an added bonus. That way, Batman has found a way to attack Superman where he is most vulnerable, using the Man of Steel's biggest weakness.