Fifteen years after a cataclysmic event known as the Second Impact, the world faces a new threat: monstrous celestial beings called Angels invade Tokyo-3 one by one. Mankind is unable to defend themselves against the Angels despite utilizing their most advanced munitions and military tactics. The only hope for human salvation rests in the hands of NERV, a mysterious organization led by the cold Gendou Ikari. NERV operates giant humanoid robots dubbed Evangelions to combat the Angels with state-of-the-art advanced weaponry and protective barriers known as Absolute Terror Fields. Years after being abandoned by his father, Shinji Ikari, Gendou's 14-year-old son, returns to Tokyo-3. Shinji undergoes a perpetual internal battle against the deeply buried trauma caused by the loss of his mother and the emotional neglect he suffered at the hands of his father. Terrified to open himself up to another, Shinji's life is forever changed upon meeting 29-year-old Misato Katsuragi, a high-ranking NERV officer who shows him a free-spirited maternal kindness he has never experienced. A devastating Angel attack forces Shinji into action as Gendou reveals his true motive for inviting his son back to Tokyo-3: Shinji is the only child capable of efficiently piloting Evangelion Unit-01, a new robot that synchronizes with his biometrics. Despite the brutal psychological trauma brought about by piloting an Evangelion, Shinji defends Tokyo-3 against the angelic threat, oblivious to his father's dark machinations.

After the murder of her father, Ryuuko Matoi has been wandering the land in search of his killer. Following her only lead—the missing half of his invention, the Scissor Blade—she arrives at the prestigious Honnouji Academy, a high school unlike any other. The academy is ruled by the imposing and cold-hearted student council president Satsuki Kiryuuin alongside her powerful underlings, the Elite Four. In the school's brutally competitive hierarchy, Satsuki bestows upon those at the top special clothes called Goku Uniforms, which grant the wearer unique superhuman abilities. Thoroughly beaten in a fight against one of the students in uniform, Ryuuko retreats to her razed home where she stumbles across Senketsu, a rare and sentient Kamui, or God Clothes. After coming into contact with Ryuuko's blood, Senketsu awakens, latching onto her and providing her with immense power. Now, armed with Senketsu and the Scissor Blade, Ryuuko makes a stand against the Elite Four, hoping to reach Satsuki and uncover the culprit behind her father's murder once and for all.

The year is 2006, and the halls of Tokyo Prefectural Jujutsu High School echo with the endless bickering and intense debate between two inseparable best friends. Exuding unshakeable confidence, Satoru Gojou and Suguru Getou believe there is no challenge too great for young and powerful Special Grade sorcerers such as themselves. They are tasked with safely delivering a sensible girl named Riko Amanai to the entity whose existence is the very essence of the jujutsu world. However, the mission plunges them into an exhausting swirl of moral conflict that threatens to destroy the already feeble amity between sorcerers and ordinary humans. Twelve years later, students and sorcerers are the frontline defense against the rising number of high-level curses born from humans' negative emotions. As the entities grow in power, their self-awareness and ambition increase too. The curses unite for the common goal of eradicating humans and creating a world of only cursed energy users, led by a dangerous, ancient cursed spirit. To dispose of their greatest obstacle—the strongest sorcerer, Gojou—they orchestrate an attack at Shibuya Station on Halloween. Dividing into teams, the sorcerers enter the fight prepared to risk everything to protect the innocent and their own kind.

Haruyuki Arita is an overweight, bullied middle schooler who finds solace in playing online games. But his life takes a drastic turn one day, when he finds that all his high scores have been topped by Kuroyukihime, the popular vice president of the student council. She then invites him to the student lounge and introduces him to Brain Burst, a program which allows the users to accelerate their brain waves to the point where time seems to stop. Brain Burst also functions as an augmented reality fighting game, and in order to get more points to accelerate, users must win duels against other players. However, if a user loses all their points, they will also lose access to Brain Burst forever. Kuroyukihime explains that she chose to show Haruyuki the program because she needs his help. She wants to meet the creator of Brain Burst and uncover the reason of why it was created, but that's easier said than done; to do so, she must defeat the Six Kings of Pure Color, powerful faction leaders within the game, and reach level 10, the highest level attainable. After the girl helps Haruyuki overcome the bullies that torment him, he vows to help her realize her goal, and so begins the duo's fight to reach the top.