The Black Abyss begins based on what they have told the MC and ML about. They originally had no plans to create the organization but began it later to protect ability-holders who weren't connected to the government. They are overall good guys who protect their members, minimize damage to their surroundings, and avoiding killing or stealing other people. As far as we know, they've never even killed a human. In the books, they were this fearsome organization that fills everyone with dread, so the government, who knows the truth, will even threaten to send their prisoners to the Black Abyss for interrogation... Not knowing anything, those people spill the beans because they're terrified of the book's version of the Black Abyss. The leaders of the Black Abyss are good guys who generally protect the weak and only fight those who attack them first. Don't attack them, and they're pretty nice.
Instead of being enemies with the Chinese government, they actually work together and rely on each other quite a bit.
The book's protagonist has nothing but a gang of transmigrators around him trying to gain his favor and control him. Although a couple of people try to do that with the MC and ML, they're generally too chicken to try taking advantage of the "villains."
The monsters of the other world show up ahead of schedule and confuse all of the transmigrators' timelines.