This. The story hinges on this whole "Revolutionary Club" but there's no fucking way a group that large formed with ZERO governmental notice, especially after the number of crimes, murders, and missing people. This series is such dogshit.
Sadly a bit of truth in fiction, Japan is kind of notorious for letting obvious dangerous cults get away with crazy bullshit until they overstep some arbitrary line and only
then do they intervene. To be fair it isn't just Japan though but a lot of East Asian countries due to cultural influence (China, South Korea, Indonesia, etc).
Like a pretty big example would be the Aum Shinrikyo cult that carried out the Saren Gas attacks in Tokyo. That wasn't even their first Terrorist attack let alone the first time they were found doing fucked up shit. Hell it's so common there is an entire sub-story in the Yakuza games that highlights the problem and how absurd it is (spoiler: the police never get involved, the protagonist has to handle it with their fists as per usual).
Then there was that more recent nonsense that ultimately led to the assassination of Shinzo Abe with the Unification Church. A slightly older similar corruption in government thing involved a South Korean moon goddess cult. Hell even the west isn't immune to this shit, you have high profile examples like Heaven's Gate, Branch Davidians, People's Temple or how about the ones that are still currently active and has faced very little legal repercussions like the Church of Scientology. People are oddly lenient when it comes to matters of "religion" and use kiddy gloves more than they really should because they don't want to step on anyone's toes despite the fact that there is a copious amount of evidence that these "religions" do some fucked up shit to their followers let alone dissidants.