Kaito is in prison after helping Kei escape. He encounters prisoners ganging up on another prisoner after a successful escape attempt. The prisoner wants no help from Kaito. It begins to be clear the prisoner is hiding something.

Kei continues his training. Tosaki attempts to get the Minitser's schedule. The Minister refuses, which leads Tosaki to attempt to steal it. However, the American investigators interfere.

Tosaki has been captured. Izumi rushes back to the hideout and insists they rescue him. Initially refusing, Nagai ultimately leads a team to rescue Tosaki from the Americans.

Nagai and the group pursue the Americans and Tosaki. Izumi manages to catch up with them and ultimately rescue Tosaki. Unfortunately, this means they missed their window to catch Sato.

Tosaki manages to get his team allowed into the building where Sato's next target is. Just as the clock ticks closer, a truck rushes in and sets off an E.M.P. bomb, rendering all electronics and new anti-Ajin guns useless. Sato charges in for an old fashioned gun fight.

Ajin are humans that cannot die. Seventeen years ago, they first appeared on a battlefield in Africa. From then on, more of their kind are discovered within the human society. Their rarity in appearance means that, for experimental purposes, the government will generously reward anyone who captures one. In the present day, for what a certain high school student expects to be a typical summer holiday, his life is about to turn unexpected...

Nagai and the group return after being defeated by Sato. Nagai struggles to deal with his failures. Sato continues towards his third and final wave, an Ajin run Japan. Tosaki tries to mobilize everyone once more to stop Sato, but Nagai refuses.

Unrest begins as Satō-san releases a chemical weapon onto the population. People begin trying to attack the families of Ajin. Nagai saves his sister with the assistance of Kaito. Nagai entrusts his sister into Kaito's care.

People from Satō's group desert and make contact with Nagai. The US plans on releasing the chemical weapons on Satō in the sewers. Tosaki is called and asked for assistance, which leads Nagai and the group to go after Satō once more.

Although he was caught off his guard, Sato has one last plan: to kill the rest of the team.