A catastrophic earthquake has left Tokyo, and most of the Earth for that matter, under the sea. Aika is a salvager who retrieves various remains from the watery ruins. When Aika accepts the dangerous mission of locating and obtaining the mysterious Lagu, she discovers that she's not the only one after it.

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.

Meg, faithful and gentle, Jo, independent and energetic, Beth, quiet and shy, Amy, amiable and precocious–the four sisters live vigorously and happily at home with their gentle mother while waiting for their father to return from the Civil War. Helping each other, they challenge their fates and grow up to become wonderful women.

Individuals who can materialize weapons from their soul are called Blazers, and they attend Kouryou Academy High School in order to harness their abilities. Each student is required to partner with another, in the hopes that one day, the pair can attain the power of Absolute Duo. Tooru Kokonoe hopes to attend this academy in order to gain power after his sister and friends were slain by a mysterious man. However, at the opening ceremony, he is forced to duel against the person sitting next to him, with the loser being expelled. As Tooru prepares to give the match his all, it is not a weapon that manifests from his soul, but a shield, an irregularity which catches the attention of a foreign student named Julie Sigtuna.