"Shangri-La" is set in a dystopian future where environmental collapse has led to severe climate change, forcing humanity to adapt to a drastically altered world. The story unfolds in a world where Tokyo has been transformed into a jungle due to unchecked global warming, and society is divided between the wealthy elite living in the climate-controlled city of Atlas and the impoverished masses struggling to survive in the ruins below. The narrative centers on Kuniko Hojo, a young girl from the slums of Duomo, who becomes a key figure in the resistance against the oppressive government of Atlas.

Kuniko is chosen as the successor to the leadership of Metal Age, a resistance group fighting for equality and justice. Her journey is intertwined with the mysterious project known as "Shangri-La," a government initiative aimed at creating a utopia for the elite while further marginalizing the poor. As Kuniko rises to prominence, she discovers her connection to the project and the true intentions behind it. The series explores themes of environmental degradation, social inequality, and the struggle for power, as Kuniko and her allies navigate a complex web of political intrigue and personal sacrifice.

Key characters include Momoko, Kuniko's loyal friend and fellow resistance member; Mikuni, a high-ranking official in Atlas with a hidden agenda; and Takehiko, a scientist whose research plays a crucial role in the unfolding events. The plot delves into the moral ambiguities of leadership, the cost of revolution, and the impact of human actions on the environment. Through its intricate storyline and character dynamics, "Shangri-La" presents a thought-provoking exploration of a future shaped by ecological and societal collapse.