Zetsubou No Shima gave us lots of information about this. But also these two ciphers: SPOILERS ALERT I DONT KNOW HOW TO HIDE TEXT SO THE FOLLOWING SENTENCES INCLUDE SOLVED CIPHERS:
"I shut down the power for the night. we must conserve the gasoline, so i am told, because the Emperor is in doubt of the usefulness of our research here at the Rising run Facility, and that resupplying the facility will now occur every other month rather than our usually scheduled weekly drops. Hopefully, the new meteor site produces higher grade samples, ones we can actually use. Wait is that a plane I hear. The resupply is not scheduled for another week. I see a bright light in the sky..."
This is probably written by a Division 9 member in the Rising Sun Facility. The Emperor doesn't think the investigating of 115 is usefull, and reduces the resupplies. But then we got this cipher:
"While the loss of the Rising Sun Facility was unfortunate, the Emperor was so impressed with our final results that he has approved the construction of the new Division 9 facility on the island we selected. He assured me personally that he will spare no expense in advancing our research. You and I both know that what we accomplish at this new facility will win the war for Japan."
Somehow, the Rising Sun Facility is gone (abandonned, destroyed, captured, I don't know what happened). But Division 9 did their job: The Emperor is convinced that their technology with 115 will help Japan win the war. So let a new facility built for them: Zetsubou No Shima. Finally, we've got this cipher:
"Although we have tried to eliminate him making it seem as if he were killed in an accident, he has managed to escape every time by some miracle. The fact that he is regarded as a hero by the commoners is unbearable, and it shall eventually led to the existence of myself being questioned. He taints the commoner’s belief in myself, I who should be held in the highest regard by them. But it is no longer necessary for me to bear this suffering any longer. I have given the order to the operatives in the 9th division/plant/facility. They must not let Masaki Takeo leave the island alive."
This is written by the Emperor about Takeo Masaki. He hates Takeo, but Takeo is a hero for the Japanese citizens? I don't know what to think of this cipher, but looking at this post you made it seems you have a good sight at the story of Takeo and Division 9. Whatcha think?