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.

Shinji Ikari is left emotionally comatose after the death of a dear friend. With his son mentally unable to pilot the humanoid robot Evangelion Unit-01, Gendou Ikari's NERV races against the shadow organization SEELE to see who can enact their ultimate plan first. SEELE desires to create a godlike being by fusing their own souls into an Evangelion unit, while Gendou wishes to revert all of humanity into one primordial being so that he can be reunited with Yui, his deceased wife. SEELE unleashes its military forces in a lethal invasion of NERV headquarters. As SEELE's forces cut down NERV's scientists and security personnel, Asuka Langley Souryuu pilots Evangelion Unit-02 in a desperate last stand against SEELE's heaviest weaponry. The battle rages on, and a depressed Shinji hides deep within NERV's headquarters. With the fate of the world resting in Shinji's hands, Captain Misato Katsuragi hunts for the teenage boy as society crumbles around them.

Eccentric and blunt, the walrus Hiroshi Odokawa lives a relatively normal life. He drives a taxi for a living, and there he meets several unique individuals: the jobless Taichi Kabasawa who is dead-set on going viral, the mysterious nurse Miho Shirakawa, the struggling comedic duo "Homo Sapiens," and Dobu, a well-known delinquent. But Odokawa's simple way of life is about to be turned upside down. The case of a missing girl the police have been tracking leads back to him, and now both the yakuza and a duo of corrupt cops are on his tail.

October 4 marks the fateful day when a high school girl vanished, triggering an unpredictable series of events. In order to unravel the mystery behind the girl's disappearance, all of the key witnesses connected to the case recount the events leading up to and following the crime. As the pieces to the story come together, they all seem to be connected to one individual—taxi driver Hiroshi Odokawa.