The 2013 live-action film 009-1: The End of the Beginning is a Japanese adaptation of the manga series created by Shotaro Ishinomori. The story is set in an alternate reality where the Cold War never concluded, continuing for over a century and dividing the world into two opposing superpower blocs: the West and the East. This prolonged period of tension and espionage serves as the backdrop for the narrative.

The central character is Mylene Hoffman, a top agent for the Western bloc known by the codename 009-1. An orphan from the Eastern sector who was recovered and raised in the West, Mylene has been transformed into a powerful cyborg, her body enhanced with various covert weapons and superhuman capabilities to serve in the Zero Zero Organization, a secret intelligence agency. At the outset, she is on a mission to dismantle a human trafficking ring, a task she handles with notable composure and lethal efficiency. During this operation, she rescues a young man named Chris, who seems to be a captive. Chris hums a lullaby that triggers deep, fragmented memories from Mylene's childhood, specifically of a brother named Paul from whom she was forcibly separated.

Mylene's primary mission quickly becomes the retrieval of a missing scientist, Dr. Klein, the woman who originally transformed her into a cyborg and serves as a mentor figure. After a failed rescue attempt where Dr. Klein is recaptured by a formidable female cyborg operative, Mylene is stripped of her agent status. She continues her search independently, driven by a need to find her creator and understand her own past. The trail leads to a confrontation where she discovers that Dr. Klein has been working as a double agent, developing advanced technology based on creating artificial life. The most jarring revelation concerns Chris, who is unmasked as Loki, a master spy from the Eastern bloc. Loki is in fact Mylene's long-lost brother, Paul, now grown and an enemy agent.

The narrative arc follows Mylene as she is forced to confront her manufactured identity and her suppressed history. Her mission evolves from a straightforward espionage assignment into a personal and psychological trial, pitting her against her own creator and her estranged brother. The climax involves Mylene battling the advanced cyborg created by Dr. Klein and confronting Loki directly. She ultimately destroys the enemy cyborg and kills her brother, completing her mission by retrieving Dr. Klein's brain to bring back to her superiors. The film concludes by reinforcing Mylene's status as a uniquely effective, if emotionally scarred, mechanical agent, having severed the last ties to her human past.