The agents of 009-1 are called on a mission to rescue a scientist from Eastern Block or at least get his data. When they get there, they find the Eastern Block agents already had the information of their arrival.
When a little, psionically active, girl is the target of a mutant hunting squad, Agent 009-1 is called in. When the girl's parents are killed in front of her, 009-1 witnesses a secret the little girl has.
An assassin called "Egg" is a new threat for the agents and when several of them are killed, 009-1 is called in to stop Egg before he can kill her.
009-1 is invited to a castle, to find a missing scientist. Western and Eastern Block supplies agents of their own as they make their through the castle. However, when people start dying, there are only two survivors to finish the mission.
009-1 goes to Rome and meets a girl who is being chanced. She helps the girl and meets 009-4 where she learns the girl is actually a android made of gold and 009-1 must stop her.
When an old friend of 009-1's retires, the Eastern Block chase after him for a painting from a child he possesses. He asks 009-1 for help and she agrees.
009-1 chases down a defector suspected of selling secrets. She meets a boy and later finds out that his grandfather and a female spy are using the boy to get the secrets out by boats.
009-1's past is revealed when the board contemplates if 009-1's emotions are getting in the way of her ability to complete missions.
In a gunfight, 009-1 manages to kill a man whose last words were "Little Billy, I am sorry". She recovers, but is taken by bikers. She is rescued by a man and his family. The man talks about how his brother used to call him "Little Billy".
009-1 is sent on a information seeking mission where she has to gather intel on the Eastern Block and their movements on studying mutant children. In a result, their is a nuclear explosion on the moon and a note threatening a lot more destruction.
The Eastern Block arrive to the facility 009-1 is at and when 009-1 decides to stay with the children rather then evacuating, Dr. Green tells her of another way. She is pitted in a battle with the Eastern Block. Loki comes to her side.
In the series finale, 009-1 finds out the kids went to the moon and Dr. Green is killed when she gets there. Loki tries to get the missiles launched to force peace, but 009-1 fights him. She learns a valuable secret regarding her past.