"Origin ~Spirits of the Past~" is set in a post-apocalyptic future where humanity's reckless genetic experimentation has led to the collapse of civilization. The Earth is now dominated by a sentient forest known as the Forest, which has evolved to possess its own consciousness and will. The remnants of humanity live in isolated cities, struggling to survive in a world where nature has turned hostile.

The story centers on Agito, a young boy living in Neutral City, a settlement built within the ruins of a once-thriving metropolis. Agito's life takes a dramatic turn when he accidentally awakens a girl named Toola from a cryogenic sleep. Toola, who hails from the pre-apocalyptic era, is bewildered by the drastically changed world and seeks to understand her place in it. Her arrival sparks tension between the humans and the Forest, as she becomes a key figure in the struggle for balance between the two forces.

Agito and Toola form a bond as they navigate the complexities of their world. Agito is deeply connected to the Forest, having been granted enhanced abilities by its spirits, while Toola represents humanity's past and its potential for both destruction and renewal. Their journey leads them to confront Shunack, a former soldier who seeks to exploit the Forest's power to restore humanity's dominance. Shunack's actions threaten to reignite the conflict between humans and the Forest, putting the fragile equilibrium at risk.

As the story unfolds, Agito and Toola must grapple with their own beliefs and the consequences of their choices. Agito's loyalty to the Forest is tested as he seeks to protect Toola and prevent further devastation. Toola, in turn, must reconcile her desire to reclaim the past with the reality of the present. The narrative explores themes of environmentalism, the consequences of human ambition, and the possibility of coexistence between humanity and nature.

The climax sees Agito and Toola confronting Shunack in a final battle that determines the fate of both the Forest and humanity. The resolution emphasizes the importance of harmony and mutual understanding, leaving the future of the world open to interpretation. The characters' growth and the evolving dynamics between humans and the Forest drive the narrative, creating a thought-provoking exploration of humanity's relationship with nature.