NIN is presumed to be controlled by an org in the US. Under Ninja is suspected to be controlled by the Prime Minister.
90% of NIN currently reside within Japan and for seventy years, since WW2, the Prime Minister has not taken control of them. They are only allowed to operate in Japan under certain conditions.
Because of this, there is a dichotomy of power between NIN and the Central Government. Which the latter hates.
During the 22-2-22 incident it was revealed that the Prime Minister used the hostage situation as a pretext to eliminate his political rivals, who were taken hostage. An hour before the Special Forces penetrated the Embassy, 16 Ninja had already infiltrated and neutralized the terrorists without bloodshed. When NIN asked the operation to be called off they were ignored and it was carried out shortly after. This resulted in the deaths of 5 Ninja at the hands of 200 Special Forces. As well as, 1 Hostage, 2 Special Forces, and 15 Terrorist.
Since NIN has been in the shadows for seventy years their intelligence network has suffered, thus they had the Genin infiltrate the high school because it is the base for the Nakano School which was an intelligence group during WW2. NIN was attempting to infiltrate the group in hopes of gaining information that would lead them to Under Ninja.
UN knows this, and since 2¥/Enkou has operatives in the school, they intend to use this to their advantage. Because NIN has agreements with the Police and the Ministry of Defense, they are not allowed to use tech that is fully spec'd.
The reason for this is that the Central Government is actually afraid of NIN's capabilities and fears they will gain the upper hand from them.
UN intends to slaughter within the school in order to frame NIN. Since, 2¥/Enkou work for the Central Government they know what NIN is and is not allowed to do. So, the goal of UN is to cause conflict between NIN and the Central Government and incite a war by making it seem as if NIN has breached their agreement. That is why the Gyaru mistakenly say NIN when Saruta, the recent UN recruit, starts to kill. As well as it being emphasized that full invisibility tech is prohibited.
UN is attempting to eradicate NIN by pitting them against the other forces of the Central Government such as the Ministry of Defense, the Ministry of Health, Labor and Welfare, and The Second Sector of Covert Operations.
Chapters:
1, 7, 23, 36.5
There might be more but I'm not double checking the chapters.
Also, it might not exactly match what the chapters say. Simply because I tried re-translating from raws and re-reading chapters in order to figure this out better. I'm about 85% certain this is the gist of what is happening.