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.

Enju is treated like an outcast at her school when it is found out that she is one of the Cursed Children, who have the Gastrea virus within them. Despite her sadness, they go look for the host Gastrea. She gives it her all and instantly is able to recover the case...

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 Tendo Civil Security Agency gets a job from Seitenshi. The job is to act as her bodyguard. Rentaro isn't very fond of the idea, but notices odd activity when it's revealed that Seitenshi will be meeting with the head of the Osaka Area while Kikunojo is gone.

Seitenshi's vehicle is hit by a sniper while she in enroute to her meeting. Rentaro realizes this is more than a mere assassination attempt and gets help from Miori to find out more about the attack.

Rentaro gets hurt trying to protect Seitenshi from the sniper. The security plan that Seitenshi's bodyguards had set up were leaked to the sniper. Enju had gone after the sniper and falls into a coma.

Rentaro had set up an outdoor classroom for the kids in the outer district and was enjoying class. Seitenshi suddenly appears and lets him know that one of the Monoliths is about to be destroyed.

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.

Before the battle against Aldebaran, Rentaro and Enju enjoy the outdoor class with the girls of the Outer District. Because the girls have very little hope and are unsure of their future, Rentaro takes them to a place where humanity had won their last battle against the Gastrea. Only three days remain until the destruction of the Monolith.

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.