The story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war's aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section's Daisuke Aramaki encounters Motoko Kusanagi, the cyborg, wizard-level hacker assigned to the military's 501st Secret Unit. Batou, a man with the "eye that does not sleep," suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute's murder. Motoko herself is being watched by the 501st Secret Unit's head Kurutsu and cyborg agents.

Love Momozono is a 14-year-old student at Yotsuba Junior Highschool that tends to care more for others than for herself. One day she visits a show of the famous dance unit "Trinity" and decides to become a dancer, too. On the same event, subordinates of the Labyrinth Kingdom show up who want to collect the unhappiness of the audience. Love gets the power to change into Cure Peach and fights them. Soon after, she is joined by her good friends Miki, who is Cure Berry, and Inori, who becomes Cure Pine.

As high school reaches its midpoint, Koichi Asakura—who dreams of studying design at art school—has his plans shaken by explosive graffiti on a museum wall. The artist is Eren Yamagishi, a left-handed girl who buried her talent after a past incident. Drawn together by art, Koichi pursues design as Eren returns to painting, but fear, ambition, and old scars threaten their paths.