January 2118. Chief Inspector of the Criminal Investigation Department, Akane Tsunemori, receives a report of an incident on a foreign vessel – the body of Professor Milicia Stronskaya has been discovered. Behind the incident is a group known as the Peacebreakers, a foreign paramilitary organization and a new outside threat who are targeting the professor's research papers known as the "Stronskaya Document". Reunited with Shinya Kogami, a former fugitive from the Criminal Investigation Department, Akane grapples with a case that quickly escalates beyond their expectations. The Stronskaya Papers could reveal a truth that would shake Japan's government, and even the Sibyl System, to the core. It is in this untold story that the missing link is revealed.

A young engineer, Tetsurou Okino, is transferred to a vermin extermination company called Hato Industries with the new robot Bullbuster that he developed himself. There, Hato Industries, a small company with little money, and its president Tajima are against a mysterious creature. There are fuel costs for robots, labor costs for pilots, and of course, wasting even a single bullet is unacceptable. Between their ideals of extermination and the reality of budgets, what does the future hold for Hato?

Years ago, astronaut Byakuya left behind precious materials in the belief that his son, the scientifically-gifted Senkuu, would one day find them. In the present, the Kingdom of Science's Kohaku and Ginrou have infiltrated the harem of the Petrification Kingdom’s leader with the help of Amaryllis, a local girl. At first, their mission progresses without a hitch. Unfortunately, an error enacted by Kohaku and Ginrou leads Minister Ibara and the Island’s strongest warrior, Moz, to identify the intruding duo as enemies. Even worse, Moz tails Amaryllis when she returns to inform Senkuu of the news, discovering the scientist's secret hideout. However, Moz's agenda does not align with Ibara's—he wants to dethrone the minister and keep the petrification device for himself. If Senkuu plays his cards right, he could gain a powerful ally and win the war once and for all.

Rami Nana-Hikari's adventures continue as the keeper of the Secret Treasure. A year has passed since the apocalyptic disaster which left a great crater in the center of Edo City. The destruction wrought major economic consequences and while much investment was poured into the public works for the new Edo Castle, the citizens were all feeling the pinch of the recession.