Danny made himself known to the world by hacking into the Justice League's communications line. Amity was safe but he was so tired of being ignored that the moment he figured out how to isolate his small town from the rest of the world he decided to let the heroes know they had failed.
He posted all the ignored calls, the GIW legal documents, the experiments, everything that would let them know that they had failed. Because he had saved himself and the others but never got help.
In a very short time Amity declared itself independent, similar to Atlantis or Themyscira; they didn't need anything from the rest of the world anyway.
At first the League thought it was the attack of a villain or some new organization.
It became very obvious that this was not the case the more they confirmed the information presented, from a law passed under their noses to the threat of exterminating an entire race of beings that were much stronger than them but decided to chose a peaceful route instead of just destroying everything.
For the first time in years, the League felt useless. The weight only increased when the last piece of "evidence" turned out to be the death certificate of Daniel Fenton, the first victim of the whole mess.