"Appleseed" is a science fiction anime series set in a post-apocalyptic world where humanity has rebuilt society in the utopian city of Olympus. The city is governed by an advanced artificial intelligence system called Gaia, which works in tandem with a council of human leaders to maintain peace and order. The story centers on Deunan Knute, a skilled soldier, and her partner Briareos Hecatonchires, a cyborg and former human. Both are members of ESWAT, an elite counter-terrorism unit tasked with protecting Olympus from internal and external threats.

The narrative explores the fragile balance between humans and bioroids, genetically engineered beings designed to assist in rebuilding society. Bioroids are emotionless and lack the capacity for reproduction, which creates tension as some humans view them as a threat to humanity's future. Deunan and Briareos are drawn into a conspiracy involving rogue factions within Olympus that seek to destabilize the city's governance. Their missions often involve confronting terrorists, rogue bioroids, and political extremists who challenge the harmony between humans and bioroids.

Throughout the series, Deunan struggles with her own identity and humanity, particularly in her relationship with Briareos, whose transformation into a cyborg has altered their dynamic. The story delves into themes of coexistence, the ethics of artificial intelligence, and the consequences of technological advancement. Key characters include Hitomi, a bioroid and close ally of Deunan, and the enigmatic leader of Olympus, who plays a pivotal role in the city's governance and the unfolding conspiracy.

The plot is driven by high-stakes action sequences, political intrigue, and philosophical questions about the nature of humanity and the role of technology in shaping society. The series balances its exploration of these themes with a focus on the personal struggles and growth of its characters, particularly Deunan and Briareos, as they navigate the complexities of their world and their roles within it.