El 16 de juliol del 1988 una explosió enorme destrueix Tòquio i origina la Tercera Guerra Mundial. El 2019, 31 anys després de l'explosió, la ciutat ha estat reconstruïda i rebatejada amb el nom de Neo-Tòquio. A Neo-Tòquio, en Shotarō Kaneda és el cap dels "Càpsules", una banda de motoristes (bōsōzoku) que es baralla amb una banda rival anomenada els "Clowns" (Pallassos). Durant una d'aquestes baralles en Tetsuo Shima, el millor amic d'en Kaneda, té un accident i queda ferit quan es creua amb en Takashi, un "esper", un individu amb poders de percepció extrasensorial i amb aspecte de patir de progèria.

The story takes place in the year 2034, two years after the events in Ghost in the Shell: S.A.C. 2nd GIG. Female cyborg Major Motoko Kusanagi has left Public Security Section 9, an elite counter-terrorist and anti-crime unit specializing in cyber-warfare, which has expanded to a team of 20 field operatives with Togusa acting as the field lead.

This coming-of-age story from Japan opens just after 17-year-old Sataka has gotten dumped by her boyfriend. When her mother is hospitalized with a malignant stomach ulcer, Sataka is left alone with her emotionally repressed father; whiling away the hours one day, she comes across a love letter written to her mother 24 years earlier. Deciding to track down the letter's author, Sataka eventually finds Shinichiro (Hiroyuki Sanada), an overweight slob who was abandoned by his wife years earlier and now spends his time hanging around pachinko parlors. Determined to clean him up and reintroduce him to her mother, Sataka nags Shinchiro until he finally agrees to her demands, and a gradual friendship develops between the two as Sataka drags him to the gym and a clothing store. But once Shinchiro's makeover is complete, he turns the tables on his young friend, and when the time comes for him to meet Sataka's mother, all concerned parties find themselves embarking on a new phase in their lives.

The now 50 year old Scientific Boys Club decides to build a ship with which they plan to sail to Mars on the "Ethereal Current", curious to see if there is life on Mars.

Going through life without legs, 12-year-old Kenny is active and enthusiastic, resisting the pressure to wear prosthetic limbs. He also finds himself the subject of a documentary made by a visiting French film crew. As the production unfolds, Kenny’s parents, brother, and absentee sister bring long-simmering tensions to the surface, shaking Kenny’s delicate sense of balance. Determined to better understand his place in the world, he hits the road for a daring journey of self-discovery.