Aya Asagiri has nowhere to call her own. Bullied at school and abused by her brother at home, she spends every day wishing for death. One day, Aya happens upon a mysterious website called the Magical Girl Site.

After losing her best friend and getting hurt, Sarina Shizukume becomes a magical girl herself and vows to get revenge against Aya. Meanwhile, Aya looks for Tsuyuno and discovers she's in critical condition. Haunted by her past, Tsuyuno stops Aya from calling for an ambulance. After Aya learns Tsuyuno's secret, she cannot hold back her tears. Tsuyuno is moved by Aya's tears and resolve.

The identity of the Magical Hunter who has been killing magical girls turns out to be a magical girl called Rina Shioi. Rina does it to survive the “Tempest” and uncovers some of the site's secrets, but falls unconscious from using her stick too many times. Aya and Tsuyuno search for a healer to wake Rina up, but the new magical girl they meet is someone unexpected.

The new magical girl Nijimi Anazawa wants Rina dead, but Aya and Tsuyuno still have no way to wake Rina up from her coma. Despite this setback, Aya's life seems to be getting better after meeting Tsuyuno. Then one day, her class gets a new transfer student. It's none other than Nijimi! Aya panics, but Tsuyuno isn't there to help her.

Tsuyuno Yatsumura is another magical girl who was given a stick by the Magical Girl Site. Tsuyuno's stick can stop time. She used it to retaliate against Sarina Shizukume. Tsuyuno warns Aya. Using the stick shortens your lifespan, and that someone is killing magical girls for their sticks, and that someone is closing in.

The magical girls' plan is to wait for a site administrator to deliver a stick to a new magical girl in order to capture them, force them to reveal the site's secrets, and to find out a way to survive. They use their abilities to their fullest, and the moment finally arrives. Aya, Tsuyuno, and Rina lie in wait at the target's junior high when the administrator appears.

Aya and Tsuyuno are sent to the hospital unconscious after their deadly battle with Sarina.

The one who stole Nijimi's stick is Aya's brother Kaname. Unable to tell anybody, Aya visits Sayuki's house with Tsuyuno and the others. Meanwhile, Kaname has set a new plan in motion after taking advantage of Nijimi's feelings in order to steal her stick. Kaname has already killed and will not hesitate to kill again. Kaname heads towards Aya to kill all the magical girls and take their sticks.

Aya and the others learn that there are multiple Magical Girl Sites, each with its own administrator, and that the information Rina has on Tempest is fake. They decide to join forces with Kosame and the magical girls from a different site in order to discover the truth behind the sites and survive. But that requires teaming up with Nijimi who is still after Rina's life.

The group has come to the beach on Aya's suggestion to try to enjoy a little downtime, but Aya actually had an ulterior motive behind the trip. Aya tells Tsuyuno how grateful she is for everything she's done, and the two girls make a promise to each other. However, when they return to the beach house, they find that Nijimi's panty stick has been stolen.

Nijimi died protecting her allies from Kaname. Aya blames herself and locks herself in her room. However, Aya has changed since meeting Tsuyuno. She is going to be stronger. Tsuyuno's words help Aya get back on her feet. Watching over her is someone unexpected. A fully determined Aya appears before her friends again at Nijimi's funeral.

It seems the administrator's identity is a human girl. Tsuyuno dies protecting Aya and her friends, but she is brought back to life as a new administrator candidate. Tsuyuno is ordered to kill Aya so she can become an official administrator. Having lost her old memories, Tsuyuno attacks Aya with supernatural strength.