Mysterious immortal humans known as "Ajin" first appeared 17 years ago in Africa. Upon their discovery, they were labeled as a threat to mankind, as they might use their powers for evil and were incapable of being destroyed. Since then, whenever an Ajin is found within society, they are to be arrested and taken into custody immediately.
Studying hard to become a doctor, Kei Nagai is a high schooler who knows very little about Ajin, only having seen them appear in the news every now and then. Students are taught that these creatures are not considered to be human, but Kei doesn't pay much attention in class. As a result, his perilously little grasp on this subject proves to be completely irrelevant when he survives an accident that was supposed to claim his life, signaling his rebirth as an Ajin and the start of his days of torment. However, as he finds himself alone on the run from the entire world, Kei soon realizes that more of his species may be a lot closer than he thinks.
Kai and Ko are on the run when Kei decided they need an ally, Tosaki. By threatening Tosaki's girlfriend, who is in a coma, he brings them reluctantly into his circle. Meanwhile, Sato has announced plans for this second wave of assassinations.
Kei and Ko train their bodies and begin to develop strategies to fight Tosaki. Kei spends time talking about his IBM with Ogura, realizing Kei's ghost is an extreme abnormality. While they begin to strategize, Sato makes his next move taking down a plane with his second target.
Sato is able to assassinate another off of the list. Nagai and Tosaki begin planning their counterattack against Sato. Nagai begins to struggle with the behavior of his IBM, wondering if he himself has to change. Tosaki also let's Nagai know Kaito's current condition.
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.
Sato and his group lead their assault. Nagai and his group prepare to intercept Sato, but Sato is too well prepared. Just when Nagai thinks he has Sato, it's revealed that Sato's IBM is similar to Nagai's.
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.
Satō emerges from the rubble as he blew up an existing tunnel below to escape being crushed by Nagai's plan. Satō begins to hunt Nagai and the others as they attempt one last attempt as stopping him before the military unleashes a gas attack.