Having killed her mentor Kumo, Alice struggles to find work without an adult figure to guide her, but the Organization that hired him now wants her, and they won't take no for an answer.
Alice lives alone in Kumo's now-vacated house, with nothing but a teddy bear for company. Running low on food, money and other supplies, Alice hits the streets to find a job, but without a parent or a reference, no employer will hire her. After coming home from her job hunt, a man in a suit offers to let her join the Organization if she will give up her name. However, Kumo told her to hang on to her own name with his dying words, so she refuses.
The man responds by attacking her with a praying mantis-style technique and revealing his own codename: Kamakiri. Kamakiri nearly cuts her throat, but Alice uses her spider-like traps to kill the other assassin before he notices it. With his dying breath, he warns that other assassins from The Organization will come for her soon.
A man named "Shidemushi" comes to clean up the corpse from The Organization, and warns Alice that if she doesn't leave the house "they" own, they will legally remove her from it with the police, and she won't be able to prove who really owns it.
The next day at school, the bully from before, Tajima Yori, hits Alice hard during a game of basketball and carries her to the nurse's office. She demands that Alice tell her why she had a gun in the bathroom, but Alice refuses to talk, not wanting her to get involved.
Inside the infirmary, Alice finds that the nurse is different from the usual person, and soon discovers that she is another assassin from The Organization. She immediately tries to fight back, but finds herself paralyzed. The woman's is Sasori, or codenamed "Scorpion," and she plans to kill Alice slowly.
Sasori gloats over Alice's paralyzed body, and tells her about her hobby of collecting the screams of her victims just as they are about to die. However, Sasori is interrupted by a knock at the door. Tajima senses something wrong, and Sasori tries to shoo her away, but when she barges in to the nurse's office, Sasori decides to kill both girls instead. However, Alice regains enough control over her spider thread to move her limbs, and Sasori decides to retreat, realizing she can't win in an equal fight.
Tajima thanks Alice for saving her, and offers her food along with room and board at her place in exchange for Alice's protection, because now the assassins will be targeting her as well.
Alice arrives at Tajima's home for the night, and is surprised to find so spacious a place considering she lives alone. The next day at school, the rest of the class treats them both like outcasts, as they are eating bento with each other, but Alice still wishes to protect her while Tajima decides to stand up for her. Soon after, Tajima wanders off and disappears, as Alice receives a ransom note.
She quickly makes her way to the upper floor and finds out that a quiet classmate of theirs, Oki Mugumi, was another assassin from The Organization. Codenamed "Gokiburi," the "Cockroach," she uses ultra-sensitive feelers within her hair to sense the direction of the air and dodge all of Alice's attacks. Instead of attacking back, she offers to return Tajima and let Alice go back to her normal life if she will become her slave.
Alice slowly decides to accept Oki's demands, until she suddenly receives a call from Tajima. Apparently, she was never kidnapped, she just went outside for a smoke, and Oki left a ransom note on Alice's desk anyway. The Cockroach laughs, saying she never expected her plan to actually work this well, but Alice quickly turns on her and kicks her into a seat, then fires a bullet just inches away from her face, offering to spare her life for now.
That night, as Alice tells Tajima about what happened at her home, Oki pops up in the same room, giving herself to Alice as her slave in return for sparing her own life.
Elsewhere, the Scorpion talks to Bachi over the phone, wondering if there really is a "boss" of The Organization or if he's just pretending like there is one to do whatever he wants with the group. Bachi responds that there really is a boss, and that person is someone within the school.