Yuuji Kazami is a transfer student who has just been admitted into Mihama Academy. He wants to live an ordinary high school life, but this dream of his may not come true any time soon as Mihama Academy is quite the opposite. Consisting of only the principal and five other students, all of whom are girls, Yuuji becomes acquainted with each of them, discovering more about their personalities as socialization is inevitable. Slowly, he begins to learn about the truth behind the small group of students occupying the academy—they each have their own share of traumatic experiences which are tucked away from the world. Mihama Academy acts as a home for these girls, they are the fruit which fell from their trees and have begun to decay. It is up to Yuuji to become the catalyst to save them from themselves, but how can he save another when he cannot even save himself?

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.

After the destruction of their hometown, childhood friends Kafka Hibino and Mina Ashiro make a pact to become officers in the Defense Force—a militarized organization tasked with protecting Japan from colossal monsters known as kaijuu. Decades later, the 32-year-old Kafka has all but given up on his dreams of heroism. Instead, he cleans up the remains of the slaughtered kaijuu after they are defeated by valiant soldiers—including Mina, who has successfully achieved their shared goal. Upon meeting his new coworker, Reno Ichikawa, Kafka faces a mirror of his past self: an ambitious young man whose one desire is to fight as a member of the Defense Force. Unfortunately, the two are soon involved in a freak encounter with a rogue kaijuu. Though Kafka demonstrates his innate heroic nature and rescues Reno from certain doom, he is left gravely injured. While both men recover in a hospital, Kafka is seemingly attacked by another one of the beasts. As a result, he gains the ability to transform into a humanoid kaijuu with the strength and powers of the massive monsters menacing Japan. Dubbed Kaijuu No. 8 by the military, Kafka resolves to use his newfound gifts for the greater good. Tied together by mutual respect, Kafka and Reno set out to join warriors like Mina at the forefront of the Defense Force.

Many years before becoming the famed captain of the Survey Corps, a young Levi struggles to survive in the capital's garbage dump, the Underground. As the boss of his own criminal operation, Levi attempts to get by with meager earnings while aided by fellow criminals, Isabel Magnolia and Farlan Church. With little hope for the future, Levi accepts a deal from the anti-expedition faction leader Nicholas Lobov, who promises the trio citizenship aboveground if they are able to successfully assassinate Erwin Smith, a squad leader of the Survey Corps. As Levi and Erwin cross paths, Erwin acknowledges Levi's agility and skill and gives him the option to either become part of the expedition team, or be turned over to the Military Police, to atone for his crimes. Now closer to the man they are tasked to kill, the group plans to complete their mission and save themselves from a grim demise in the dim recesses of their past home. However, they are about to learn that the surface world is not as liberating as they had thought and that sometimes, freedom can come at a heavy price. Based on the popular spin-off manga of the same name, Shingeki no Kyojin: Kuinaki Sentaku illustrates the encounter between two of Shingeki no Kyojin's pivotal characters, as well as the events of the 23rd expedition beyond the walls.