Snowdrop appears in the underground facility as some sort of hybrid between bird and person, a strange new creature created by a super intelligent AI which no longer needed humanity to exist. Lacia attempts to hack the cloud system that stores hIE behavior controls in order to stop Snowdrop. Her efforts would determine the outcome of the entire human race.
Once again, Methode appears to stand in the way of Arato and Lacia down in the underground facility containing Higgins. They must also be wary of Snowdrop who had been sent there by a rival super intelligent AI. As the conflict escalates, Arato and Ryo try their best to fulfill their duties as representatives of humanity.
Ginga Watarai's death puts an end to the incident at the experimental city. During all of the chaos, Arato had revealed his feelings to Lacia which she accepted. Yuka has mixed feelings about this sudden new coupling within her household. Meanwhile, the security police and Lacia-class masters begin to respond to the ever-changing situation.
Methode abducts Yuka right in front of Lacia. Arato and Ryo head to rescue her, but standing in their way are all of the hIE's in the experimental city who have been infected by Ginga Watarai to act like zombies. In order to get the hIE's to regain control, Arato and Ryo head to the administration center, but...
Arato is given two weeks of suspension after the fight between Methode and Lacia leaves him with paying 4.5 million yen worth of damages they caused. In order to apologize to his father Kozo who offered to pay half of the damages, Arato takes Lacia, Yuka, and Ryo to Tsukuba where a large-scale hIE experiment is being conducted.
Having made a contract with Shiori, Methode suddenly attacks Lacia while she is filming a commercial. As the circumstances surrounding Arato and Lacia are about to shift again dramatically, a new transfer student arrives at Arato's high school. Erica Burrows-the Sleeping Princess born in the 21st Century who just awoke from suspended animation, and Arato senses animosity from her.
Arato manages to rescue Kengo from the calamity at the industrial promotion center. However, even after returning to normal life, he finds himself consumed by the ever deepening mysteries. Meanwhile at the Memeframe Corporation, a factional dispute becomes escalated. Within the upheaval, the Lacia-class hIE Methode is about to make her move.
Arato arrives at the industrial promotion center which is the target for the antibody network's terrorist attack. He heads up the stairs and sees the android politician Mikoto his father developed, which leaves him with feelings of uneasiness. Soon after, the terrorist unit led by Kouka as well as another Lacia-class hIE arrive on the scene. A big battle is about to break out!
Despite his awareness of analog hacking, Arato can't help himself from being drawn to Lacia. Amid all of this, Lacia is "kidnapped" right in front of Yuka. Arato is upset with the police and their unwillingness to treat this as anything but property theft, so he gets the help of Ryo and Kengo to investigate on their own.
After binding an owner contract with Arato, Lacia has come to live with the Endo's. Arato's sister Yuka has completely accepted Lacia, and even enters her into an hIE modeling audition. Meanwhile, Arato can't hide his apprehension with living with someone who looks to be a beautiful girl his own age.