Year 2031: Tokyo Area. Most of the human race has been wiped out by the parasitic Gastrea. Part of the Anti-Gastrea movement, high school student Satomi Rentaro works as a civil officer for Tendo Civil Securities. On a mission, he meets a suspicious man in a mask and a tuxedo: Hiruko Kagetane.

Rentaro and President Kisara head to the Defense Ministry after being summoned. All of the reputable civil officers from the Tokyo Area show up there. The one who summoned them there is Seitenshi, in regards to destroying the host Gastrea and recovering the contents of the case that's inside the Gastrea.

Hiruko instantly takes care of 29 civil officer pairs and comes face to face with Rentaro and Enju again. Rentaro shows his true power to Hiruko, proving that he's not the only one that was part of the New Human Creation Project and they battle again.

The monolith finally starts to turn white. In fear of the great destruction to follow, the people of the Tokyo Area start panicking. Meanwhile, the civil officers start gathering around Monolith 32.

The outdoor classroom is completely destroyed because of the bombing. Hope is starting to be destroyed along with the Monolith as the JASDF and Gastrea face off. However, the ones to show up at the civil officers' base were JASDF who had been turned into Gastrea themselves.

Rentaro is condemned for a decision he made in battle, and is told that there is another Gastrea named Pleiades that is protecting the already supposedly immortal Aldebaran. Rentaro is forced to face the enemy alone, and is helped by someone rather unexpected: his enemy from the past.

With the addition of Kagetane and Kohina, the adjuvant is complete. They choose the Flames of Revolution, the last place humanity won their battle against the Gastrea, as the ground for the final battle against Aldebaran.