A senior high school student finds her world turned upside down when her abusive uncle is killed by a mysterious assassin. Suddenly, she's being trained by the same assassin to do his job!
Alice Fuji is suffering from bullies at school and is about to be raped by her uncle Yoshino when he is suddenly strung up by his neck by a mysterious assassin. He then tries to kill Alice to leave no witnesses, but Alice dodges a fatal blow and responds by biting off a piece of him before falling unconscious. She later wakes up in the man's care.
He claims to be an assassin codenamed "Arachnid," and works as muscle for an enigmatic Organization that Alice's uncle owed money to. When he couldn't pay, Arachnid took his life. Alice wants to go back to what little she has left, but Arachnid stops her, saying she has a similar condition to him called "Congenital Excessive Concentration," the ability to sense everything around him at the expense of immediate, short-term thinking. Arachnid wishes to use her, so he brings her to his contact within the Organization, Suzume Bachi. But Bachi orders him to kill her.
Kumo (Arachnid) can't bring himself to kill Alice, so Bachi tells him to disappear. Instead, Kumo takes Alice to his home, and after giving her some food, begins to teach her the ways of a spider-like assassin. Alice starts to despair when she gets beaten in her first lesson, but does not have anywhere else to go.
Alice begins to train with Arachnid's custom weapon "Kumoito," a whip made of thousands of woven spider-threads with a sharp blade at the end. She uses it to sense the world outside the room. But the whip also nearly kills her when she loses concentration, making it impossible to use by anyone without the CEC ability. After training with it for a few hours, she manages to wield it without endangering herself, and then promises to help Arachnid kill Bachi.
The next day at school, Alice decides to fight back against the bullies who are dunking her head in the toilet.
Alice points a Derringer at the head bully, planning to kill her for a "rehersal," but can't bring herself to do it. Later, she meets with Arachnid on the rooftop to begin the plan to kill Bachi. However, Archnid fires a gun at her, saying she has become too strong to live.
Alice fights Kumo in a duel to the death on the rooftop, using her learned techniques to try and sense his location. In a split second, she manages to hit Kumo in the chest. With his last words, he responds that Bachi was never the target: he really wanted to see if Alice would be strong enough to kill him, since he had no use for this world. Alice finally musters up the courage to finish him off with a bullet through the head, then cries out in pain.
Elsewhere, a sniper plans to shoot Alice, but Bachi calls him off at the last second, planning to make her join the Organization instead.