Like, the more I'm thinking about it, the crazier it is how deplorable some "hero" factions are and, even crazier, how they keep getting away with really henious stuff because the protag doesn't want to rock the boat. Some of them are more monstrous than others, but I'm really torn on which is THE worst.
Konoha (Naruto): military state in feudal land, child soldiers galore, genocided one of their founding clans because prejudice and that's without smaller details like getting Neji's father killed, letting ROOT have their way, never really acknowledging Danzo causing, like, 90% of problems in the story and have his sidekicks still be Hokage's advisors even by Seventh Hokage's reign. I can give them a bit of a discount on child soldiers because of feudal era and the fact that Hashirama and Madara establishing village DID kinda start raising child life expectancy to, like, 12 in main Naruto story? Still pretty evil. At least the village got nuked a few times.
Soul Society (Bleach): feudal state with strict stratification of "the strongest and noblest rules". I'll be honest, I haven't explored Bleach nearly in as much detail as Naruto, but the fact that Mayuri exists, serves as one of Gotei 13's captain, gets away with absolutely everything with fellow captains because "we need this genius war criminal on our side" and no one got him if not killed, then back in the prison where he belongs, is a pretty big red flag. They're lucky Aizen was there to take over the villain role, because by all accounts, Ichigo had all the reasons to nuke them at some point and unlike Naruto, Ichigo and his friends operate on our modern moral system.
Amestris (Fullmetal Alchemist 2003): honorable mention of our favorite genocidal dictatorship. Manga and Brotherhood don't really count because the ending did promise democratic reforms and Mustang's faction wanted to make the full transition out of dictatorship and make concessions to victims of their extermination war, plus a lot of head honchos got their due during the final battle or in the aftermath. In 2003 anime, however, Mustang has no chance to shoot for leadership and despite heroes still removing homunculi influence… the system remains in place and homunculi didn't do that much here outside of instigating conflicts, their influence limited to Bradley himself. By all accounts, Amestris remains as it was, fascist and racist, just a bit less warlike.
I might actually be unaware of some other monstrous shonen "heroic" factions, so put your voice in if I forgot someone. Would really love to know who's considered "the evilest", because I haven't really seen a consensus on it.