Eccentric scientist Rintarou Okabe has a never-ending thirst for scientific exploration. Together with his ditzy but well-meaning friend Mayuri Shiina and his roommate Itaru Hashida, Okabe founds the Future Gadget Laboratory in the hopes of creating technological innovations that baffle the human psyche. Despite claims of grandeur, the only notable gadget the trio have created is a microwave that has the mystifying power to turn bananas into green goo. However, when Okabe attends a conference on time travel, he experiences a series of strange events that lead him to believe that there is more to the Phone Microwave gadget than meets the eye. Apparently able to send text messages into the past using the microwave, Okabe dabbles further with the time machine, attracting the ire and attention of the mysterious organization SERN. Due to the novel discovery, Okabe and his friends find themselves in an ever-present danger. As he works to mitigate the damage his invention has caused to the timeline, Okabe fights a battle to not only save his loved ones but also to preserve his degrading sanity.

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.

What happens when two people love each other but just aren't meant to be together? Takaki Toono and Akari Shinohara are childhood friends, but circumstances beyond their control tear them apart. They promise to stay in contact, and although the progression of time widens the distance between them, the chain of memories remains ever-present. Byousoku 5 Centimeter is a romantic drama that focuses on the mundane and harsh reality of long-distance relationships. Stuck in the past and unable to make any new memories, Takaki and Akari cling to the hope of seeing each other again. They live their everyday lives half-heartedly, both hurting themselves and the people around them.