One of the main appeals of Batman is his lack of superpowers. While heroes like Superman and Wonder Woman have a wide variety of powers to help them fight evil, Batman only has his intelligence, his gadgets, and an endless supply of money. His greatest asset though is his almost supernatural ability to plan ahead. This makes him a great ally to teams like the Justice League who can use that planning to fight villains that should be indestructible. Unfortunately for the League, he has plans to defeat more than just supervillains. In JLA: Tower of Babel Batman's plans incapacitate every member of the Justice League.
While the plans do originate from Batman, the Dark Knight isn't the one to enact them. In the storyline by writer Mark Waid and artist Howard Porter, Ra's al Ghul steals Batman's files on taking down the Justice League and uses them to devastating effect. Martian Manhunter, DC's strongest hero, is the first to fall as nanomachines make his skin ignite with air, burning the Martian hero. As the heroes begin to realize someone is targeting them, Aquaman is exposed to a special mixture of Scarecrow's fear toxin that gives him a deathly fear of water. A post-hypnotic suggestion then renders Kyle Rayner blind, meaning he can no longer direct his ring constructs. All of that pales in comparison to what Batman had planned for the remaining heroes.
Wonder Woman may not have a readily available weakness like many of the other League members, which makes her defeat more devastating. Nanomachines trap Diana in virtual reality and pit her against an opponent who, much like Diana herself, will never give up, meaning the two will fight until Wonder Woman faints from exhaustion. Ra's then uses nanites to make Wally West have seizures if he goes too fast. Superman's defeat is perhaps the most insidious as newly synthesized red kryptonite is used to send his super senses into overdrive, making even the tiniest sound become ear-shattering. Batman's plan to take out himself is the simplest, as all Ra's has to do is steal the corpses of his dead parents, making Bruce unable to focus on anything other than getting them back.
Inevitably, the League overcomes each individual attack and unites to stop Ra's. Though the villain's plan fails, it does succeed where few villains have before in breaking the League's trust in one another. Batman's rationale for his plan all stems from a Silver-Age story where villains took control of the League. Despite Bruce's reasoning, Wonder Woman, Plastic Man, and Aquaman are all furious with Batman for how he inadvertently caused all this. Though Flash, Green Lantern, and Martian Manhunter are similarly hurt by what happened, they do understand Batman's logic and vote to keep him in the League. Superman should be the deciding vote, but before he decides Batman's fate, the Dark Knight leaves, having already deduced that Superman would vote against him.
The set of issues is an absolute classic Justice League storyline for good reason. Batman's plans to take out the Justice League are interesting and the interpersonal conflict they cause is compelling. In the end, it's hard to not understand Batman's perspective. The DC Universe is filled with supervillains capable of brainwashing or otherwise compromising superheroes. It would be silly not to have a contingency plan for what to do in case a superhero was compromised. Of course Batman should have told the League about this before creating the plans, but that hardly seems like an offense worthy of expulsion.
Tower of Babel became such an iconic story that it has been referenced countless times in other mediums. The Flash recently saw Cisco use Batman's plan for Flash. 2012's Justice League: Doom adapts the comic with a few changes, most notably the ending. Instead of Batman being voted out, Batman outright quits, but not before Superman gives Batman a kryptonite bullet, implying that Clark still trusts his friend despite everything.
In modern comics, Batman trusts the League more than he did after Tower of Babel came out. Still, comic readers have to wonder what plans Batman has for defeating the modern Justice League.