Masane Amaha returns to Tokyo with her daughter, Rihoko, in order to start a new life. Unfortunatelly, a fight between her and some NSWF organisation members who want to separate her from her daughter, Masane is arrested.

After managing to awake the powers of the Witchblade, Masane is captured again and used as a test subject. Meanwhile, Rihoko starts searching for her mother.

Takayama offers Masane a job, but the only thing on Masane's mind is finding her daughter.

The appearance of the Witchblade draws the attention of Furumizu, the leader of the NSWF organisation. Meanwhile, Masane and her daughter start looking for a place to live.

Tozawa tries to investigate Masane, in order to find out the truth about the Witchblade. Masane refuses to talk, and is challanged to a fight by Shiori, one of the Cloneblades.

Masane is badly injured after her fight with Shiori and is rescued and taken care of by some of Dohji's men. Tozawa has witnessed the fight and decides to find out everything about the Witchblade.

Masane discovers more about Takayama's past. Meanwhile, Shiori goes berserk from over-using the Cloneblade, and decides to attack Masame one more time.

Masane is forced to use the Witchblade in front of Tozawa, when they are attacked by an ex-con.

Masane and Tozawa learn more about the ex-con's past.

Masane is forced to accompany Takayama to a party, where she must confront Wado, one of Takayama's rivals.

Maria, a new generation of neo genes, is introduced. Takayama spends a lot of time with Masane due to his hangover, but Masane goes into a panic over her daughter’s illness and the threat of a Cloneblade.

Tozawa and Takayama try their best to rescue Masane, while NSWF gathers a lot of data. How boldly will Takayama move to get Masane and the Witchblade back?

NSWF’s Child Welfare Division wants to take Rihoko away from Masane to live with her biological mother. Masane and Riko decide to run away, but Nishida sends Nora there to capture the daughter, then Reina interrupts.

Reina and Rihoko get adjusted to their life as mother and daughter, while a depressed Masane learns something about her past. And Maria receives her cloneblades.

Maria, now armed with her dual cloneblades, seeks out Reina, whom she believes is her mother. However, she doesn’t like what she finds in Reina’s apartment.

Masane gets a break from fighting and enjoy a day at a beach resort with Rihoko and their neighbours.

Masane’s bothered a great deal about Rihoko being the next successor of the Witchblade, and Father Furumizu shows he’s got some problems, as Tozawa gets information of his personal history.

Investigations to new murders and an anonymous video footage brings trouble to Douji Industries, especially to Takayama.

Masane forces herself to work with Wado for Riko’s sake, but Riko wants Masane to see Takayama. Meanwhile, Wado still sees Takayama as a threat and sends Ultimateblade Yagi to kill him.

Maria takes over the NSWF, meanwhile Masane sets up Takayama and Rihoko to go on a play date, but Takayama is a bundle of nerves and Riko can’t enjoy herself. It looks like Masane will have to join in after all. This incident makes Masane wield the Witchblade in front of her daughter.

Takayama goes to Douji to find data to help Masane’s condition. Meanwhile, Masane tries to remove the witchblade.

Masane thinks about the future for her daughter and tries to tell her about her impending death at a park. Meanwhile, Maria makes plans to grab the power of the Witchblade and Nishida/Wado send out 3 IU-Weapons to capture the Witchblade.

Masane spends quality time with Riko, Maria and Asagi head to take the Witchblade, and thousands of malfunctioning I-Weapons converge on Tokyo. Will this be the end of Tokyo?