Several agents have been killed by the hitman known as Egg. Now 009-1 is his next target. She's called in to take him out also. They travel to an island where 009-1 uses his assassination "style" against him.

009-1 has been invited to a castle along with two other Western Block agents and three agents from the Eastern Block in order to find a missing scientist. When phantoms begin appearing and agents start dying, things get interesting. The last two survivors are 009-1 and Loki.

009-1 is on vacation in Rome when she meets up with a girl who is being chased by some men. She helps her out and in the process runs into 009-4 who is staking out someone. She discovers that the woman is in fact an android made of gold and must use everything she can to bring her down.

An agent has "retired" and 009-1 is sent to get him. She remembers how, when she was new to the game, he helped her and saved her life many times. He tells her he retired because he could never paint as well as some kids' drawing he found on his last mission. Now the Eastern Block is after him for what he has and he asks 009-1 to help him out.

009-1 is searching for a defector that appears to be selling secrets. She runs into a little boy and he takes her to his house in order to get out of the rain. As things unfold, a woman spy and the boy's grandfather is using the boy to launch remote controlled ships into the bay in order to sneak out the secrets.

The board is questioning whether or not their best agent, 009-1, has too much compassion for her to continue on. We learn a little from her past and what made her what she is today.

On a mission 009-1 winds up killing a man but not before she's shot up as well. As he dies he tells "Little Billy" that he's sorry. After recuperating, 009-1 takes some time off but some biker thugs throw nails at her car and her tires go flat. A man and his family pick her up and they take her with them. Along the way they tell her about the man's brother and how good he was. After the wife and son fall asleep in the car, the man takes 009-1 to his old house and tells her about how his brother used to call him "Little Billy".

009-1 has been given an information gathering assignment at the research facility where the Eastern Block is studying mutant children. She gets to know some of the kids there. Dr Green uses the computers to somehow control the mental abilities and cause a nuclear explosion on the moon. A crayon written note arrives later telling the two nations to disarm or they'll use the "reverse-explosion" technique on any nuclear weapon in the world.

Eastern Block forces arrive at the research facility having realized that that is the most likely place the "reverse-explosion" machine is. 009-1 refuses to evacuate and stays with the kids. She learns that Dr Green has a way out and follows with the kids. Once outside she battles the Eastern forces so that the kids can escape. She gets a little help from Loki along the way.

009-1 refuses a call to return when she realizes that the kids have gone to the moon. She arrives there and finds Loki and makes him take her to where they're keeping the kids. Forces invade the place and kill Dr Green while Loki attempts to launch some nuclear missiles in an attempt to shock the world into peace. 009-1 tries to stop him but the forces arrive and shoot him - just about the same time she learns a startling secret about his true identity.