All eyes are on Utena Tenjou, a mysterious transfer student to Ohtori Academy. But Utena's eyes seem to be fixed on one familiar face that stands out among the rest—Touga Kiryuu, Utena's childhood friend. Touga knows of Utena's past and possesses knowledge of the Mark of the Rose, a set of unique rings worn by those who compete for the hand of the Rose Bride. The Rose Bride, Himemiya Anthy, belongs to whomever wins her in a duel, and the one that wins all the duels is said to be given the power to bring revolution to the world. Utena is drawn into the duels, but Touga and their complicated history together may end up unraveling everything. Nothing is as it seems in this retelling of the original anime series.

Keitaro has finally passed the entrance exams, and is officially a Toudai student. But after breaking his leg in an accident in the entrance ceremony, he thought and re-evaluated himself. Having new goals, Keitaro follows Seta on an overseas archeology trip. During his absence, however, all was not well in Hinata Lodge. Urashima Kanako, Keitaro's sister, arrives on the scene. She claims to be the new manager of Hinata Lodge starts to go against all the tenants. Things become even more complicated when they recieve a letter from Keitaro. The tenants and Kanako made a big mess trying to get the letter, but Seta's car crashes in before anyone could read the letter...

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.