While the Justice League defends the DC Universe as the premier team of superheroes working together, Batman secretly developed plans to take down each of his teammates should they ever break bad. His plan came together in the pages of JLA's issues #43-46, by Mark Waid, Howard Porter, Steve Scott, Drew Geraci, Mark Propst and John Kalisz for the acclaimed "Tower of Babel" storyline. The story arc had Ra's al Ghul distract the Dark Knight by stealing the bodies of Bruce Wayne's parents while gaining access to Batman's contingency plans against the heroes and enact them. The heroes recovered, with Batman voted out of the Justice League for a time while several members understood his decision to develop the contingencies.
Here is a recap of how Batman devised specific ways to take down each of his teammates in the 2000 storyline and how they managed to recover and stop Ra's from seizing the opportunity to remake the world in his villainous image.
Superman
Even in his contingency plans, Batman sought a way to incapacitate Superman without killing him. To that end, the Caped Crusader created an artificial form of kryptonite that had a distinct red hue. Unlike the standard red kryptonite, which would temporarily turn Kryptonians evil when caught in its aura, the artificial red kryptonite made Kryptonians' skin turn translucent and overcharged their bodies with solar energy, making them defenseless as the super-charge racked their entire body with pain.
The Man of Steel is exposed to the artificial red kryptonite, becoming engulfed in pain while he is overwhelmed by his out of control super-senses. Eventually, the effects of the red kryptonite wear off in time for Superman to destroy Ra's device scrambling language and causing widespread confusion.
Wonder Woman
Batman is well-aware that Wonder Woman is a warrior without equals and knows conventional strategies won't bring the Amazon superhero down. Instead, a nanite is injected into Diana Prince's ear, creating a vivid virtual reality program around her. In this imagined world, Wonder Woman sees an opponent at equal proficiency that battles her without surrender.
The program was developed with the intent of Wonder Woman fighting until the sheer amount of physical exertion against the projected opponent would eventually cause her to die from exhaustion. The nanite was removed from Wonder Woman, ending the program and saving the weary Amazon.
Aquaman
One of the more twisted strategies Batman developed targeted Aquaman. Using a modified strain of the Scarecrow's signature fear toxin, Batman's contingency against Arthur Curry induces severe hydrophobia into the Atlantean superhero. With Aquaman requiring regular contact with water due to his half-Atlantean physiology, Arthur's avoidance of water would cost him his life in a matter of hours.
Arthur is discovered and he is cured of his toxin-induced hydrophobia in time for him to immerse himself in water, restoring him to full strength though remaining deeply distrustful of Batman from his ordeal after the story.
The Flash
Perhaps the most painful strategy employed targeted The Flash, with Wally West shot in the back of the neck with a tiny, vibrating bullet. The vibrations not only prevented the Scarlet Speedster from vibrating the bullet out of himself but its placement in Wally's spine caused him to endure a seemingly endless series of seizures at lightspeed from the trauma.
Wally managed to short out the vibrating bullet by striking himself with a bolt of lightning, frying the projectile and regaining control of himself.
Green Lantern
For Green Lantern, Batman is forced to get more creative to incapacitate Kyle Rayner. While sleeping, Kyle's Power Ring slipped onto his finger and he is given a post-hypnotic suggestion to subconsciously use it on himself to turn blind. Unable to see after waking up, Kyle is largely sidelined as he can't create energy constructs accordingly.
After Kyle is discovered, the Power Ring is removed from his finger to sever his connection with it while the mental nature of his attack is explained to him. Now understanding what had happened to him, the hypnosis-induced blindness is broken.
Martian Manhunter
One of the cruelest strategies was employed against the Martian Manhunter, with Batman taking advantage of Martians' inherent weakness to fire. J'onn J'onzz's skin was secretly coated with magnesium nanites that burst into flames upon contact with open-air, rendering him helpless as he was set ablaze.
Due to his Martian physiology, J'onn survived the attack but was visibly shaken by the experience by the time the nanites had burned away.
Plastic Man
For Plastic Man, Batman conceived the simplest strategy to defeat the malleable, shape-shifting superhero: Freezing his body with liquid nitrogen and shattering him with a hammer.
While the frozen Plastic Man was left unceremoniously in pieces on the floor of the Justice League's headquarters, the pieces of the superhero reform after he eventually thaws out. Despite no long-lasting physical harm, the experience traumatizes Plastic Man, making him distrustful of Batman.