A young Taiwanese assassin codenamed "Glass Heart" committed suicide by jumping off a building, and her heart was pierced by metal fence. Miraculously, her life was saved by heart transplantation. During her recovery she began to experience strange dreams, which lead her to Japan looking for the donor of her heart, who happens to be Kaori Makimura, former partner of City Hunter Ryo Saeba. The author mentioned in the first tankoubon volume that Angel Heart only shares the same characters of City Hunter but not its continuation. The events are all parallel universe, therefore it has nothing to do with City Hunter.

Since childhood, Haruka Kotoura's classmates have seen her as a creepy and monstrous person. This is due to her ability to read other people's minds—the same ability that drove her parents away, leaving her alone with her grandfather. As a result, she has grown accustomed to the bitter treatment by the people around her, becoming completely cold and unsociable to others. However, everything starts to change when Haruka transfers to a new school. While most are off put by her as usual, she meets Yoshihisa Manabe, who finds her power astonishing. Yoshihisa then proceeds to befriend Haruka, promising to never leave her no matter what happens. Haruka's new experiences of social belonging thus begin, meeting new friends and learning to open herself along the way. [Written by MAL Rewrite]

The day before the ceremony marking the completion of the Yajima Stadium, Nils Nielsen invites Sei Iori, Meijin Kawaguchi, and others to an exhibition battle using the new large-scale battle system he has designed. Now that they are all reunited, Sei attempts to show off the Build Strike Cosmos that he has upgraded for the exhibition, but then he notices something missing... Meanwhile, somebody takes control of the stadium's systems, sealing Sei and the others inside. Before them appears a mysterious group, which has come to challenge them to Gunpla Battle.

Three hundred years ago, a genetic experiment gone wrong caused the mutation of all forests on Earth. Armed with consciousness, the vegetation sought to destroy all of humankind, and the war that ensued turned the planet into a hellish dystopia. In the present day, Agito, a young boy, lives with his father in Neutral City—a village maintaining an uneasy truce with the neighboring forest. One day, Agito, on his way to collect water, becomes separated from his friend and stumbles upon a relic of the past: a girl sleeping in a mysterious machine. Agito awakens the girl, Toola Cm Sacl, and introduces her to the village. But outside forces have ulterior motives for the girl, who holds the key to restore the Earth. Misguided by Shunack, a soldier from the old world hellbent on destroying the forest, Toola follows him despite Agito's warning. Determined to save Toola and unify humankind with the forest, Agito borrows the power of the forest and pursues her.