Yuko and her sister move from Kanazawa to the city of Daikoku. Shortly after arriving, their virtual dog Densuke runs through a wall and disappears.
Yuko and Fumie attempt to cure Densuke of his virus. Meanwhile, a mysterious girl dispatches an army of tiny virtual creatures to capture Densuke.
On Yuko’s first day at school, she receives word that Densuke has been kidnapped. She and Fumie go in pursuit, but they are obstructed by Searchmaton.
Yuko tries to befriend Isako but is coldly rejected. Afterward, Daichi launches a digital attack on Isako as revenge for refusing to join his club.
Isako convinces Daichi and his pals to accompany her on a search for metabugs. Yuko and Fumie team up with Biology Club head Haraken and follow them.
Determined to find out Haraken’s true identity, Fumie and Yuko investigate Searchmaton’s programming. Kyoko wants to join them in their experiments.
Yuko and Fumie’s search for a virtual pet hamster leads them to an abandoned factory, where Isako is attempting to capture a legendary illegal.
On the day of the summer festival, Isako orders Daichi to challenge Fumie to a duel. But Daichi’s feelings for Fumie make him reluctant to comply.
The kids spend the night at school. After sharing spooky stories about Michiko, they carry out their duel while Isako continues to pursue the illegal.
Isako kicks Daichi out of the club. While helping Haraken follow some mysteriously obtained directions, Yuko suddenly remembers a boy called 4423.
Aiming to obtain metabugs, Daichi captures and raises a goldfish illegal. Disaster strikes when it grows exponentially and breaks out of his house.
After disappearing for a few days, Daichi shows up at school with a digital beard made of illegals — which turns out to be highly contagious.
Yuko and Haraken spot Denpa secretly taking care of an illegal in a vacant lot scheduled for construction. The friends hurry to find it a new home.
Akira records clips of his sister Fumie to use as proof of her bullying him. Meanwhile, Haraken meets a young man investigating the events in Daikoku.
Yuko gets lost and meets a boy named Takeru. As he leads her back to the station, she comes upon an area that she remembers from her early childhood.
Yuko chances upon Akira in the hospital and catches him in the act of recording Isako. Curious, she watches the video and makes a shocking discovery.
After telling Haraken about Isako’s secret, Yuko tries to get him to open up. Tamako sets out to thwart Isako’s efforts in capturing the kirabug.
Isako opens a gateway to the other side, allowing Haraken to pass through it and attempt to find his lost friend Kanna. Yuko tries to stop him.
Yuko and Fumie narrowly escape some menacing illegals thanks to Megabaa’s barrier. Reaching safety, they seek a way to recover Kyoko’s digital body.
Haraken once again crosses over to the other side. As Tamako and Yuko go in pursuit, Tamako tells Yuko about a terrible mistake she made in her youth.
As the new school semester starts, Yuko is worried about the still bedridden Haraken. Meanwhile, Isako is harassed by a group of boys at school.
Yuko rescues Isako from a new Searchmaton and they escape to the Okonogi household. Isako takes a look at Densuke and discovers a secret about him.
Isako, Yuko and Daichi are chased by Searchmatons during a large-scale reformatting of the city. Nekome orders Isako to use Densuke to open a gateway.
After hearing about what happened to Isako, the children’s parents confiscate their glasses. Meanwhile, Tamako searches for a way to save Isako.
Using her deceased grandfather’s glasses, Yuko enters the gateway and follows the pain in her chest to search for Isako. But trouble isn’t far behind.
The mysteries surrounding Michiko and 4423 finally unravel as Yuko’s memories return. With no time to lose, Yuko hurries to save Isako’s digital body.