Po przeprowadzce do pełnego technologii miasta Yuko razem z innymi dziećmi dołącza do agencji detektywistycznej swojej babci, która szuka zaginionych dzieci.
[Netflix]
Yasako and Fumie ask Yasako's grandmother, Megabaa, to cure Densuke of a deadly illness. In return Yasako agrees to join Megabaa's Detective Agency as their eighth member. Meanwhile, Yuko Amasawa (nicknamed Isako) relentlessly searches for the "Keyhole". Deducing that it resides as an illegal in Densuke, she unleashes her virtual pets to capture him.
Having captured Densuke, the Mojos deliver him to Isako. After separating the illegal from Densuke, Isako unsuccessfully attempts to "unlock" the organism with her key, causing nearby cyberspace to rupture. She reports the event to a mysterious conspirator over the phone.
A frenzied cyber battle breaks out at school between Isako, Fumie, and Daichi Sawaguchi's group, the Daikoku Hackers' Club. While Isako is the ultimate victor with Daichi's group completely subdued, Fumie manages to steal a piece of data from Amasawa that is totally corrupted with exception of the word "Michiko".
Isako leads the beaten and desperate Daikoku Hackers' Club on a metabug expedition over the fringes of Daikoku's cyberspace. During the expedition, Isako traps and assumes control of the Daikoku Hackers. Captivated by Isako's skill, Daichi asks to become her disciple.
Yasako and Fumie begin an investigation into Haraken and Searchmaton. They attempt to test and map out Searchmaton's behavioral patterns and programming. Under pressure, Haraken reveals to Yasako and Fumie his familial connections to the administrators of Searchmaton and his motive for investigating viruses and illegals.
Isako once again summons the illegal with the help of the Daikoku Hackers. However her plans are inadvertently disrupted by the pet detectives Yasako and Fumie working on an unrelated case. Isako eventually chases the rogue virus to a corrupted space on the school grounds.
Isako hatches a plan and asks Daichi to challenge the Coil detectives to a duel. Daichi, at the expense of his revived friendship with Fumie, reluctantly complies. Haraken recovers a mysterious metabug from his former research partner's lost pet.
The kids spend a dark and stormy night at school telling ghost stories and playing spooky cyber games. Isako uses the distraction to capture a kirabug manifested in the form of Michiko inside the school. Meanwhile, Haraken is briefly whisked away to "the other side".
Haraken, Fumie, and Yasako follow clues left by Haraken's former research partner, Kanna Ashihara. Meanwhile, Daichi is ejected from Isako's group due to his failure to defeat Fumie in a duel. Yasako remembers a meeting with 4423 from her childhood.
With the help of Kyoko, Daichi, in a plot to acquire metabugs, catches and raises a fish-type illegal as a virtual pet. He eventually loses control of it as it floods Daikoku City with digital water. Megabaa's history with Tamako is discovered as they have to team up to stop the illegal.
The protagonists find a race of microscopic illegals growing on their faces. Yasako, utilizing a communication device devised by Megabaa, becomes heavily engaged in a god game-like relationship with the developing civilization. She attempts to use her divine influence to save the war-mongering race before it crumbles from a nuclear holocaust. In the wake of devastation, the illegals set out to find their "homeland".
The protagonists agree to aid Denpa in relocating a docile plesiosaur-type illegal, which he had previously been raising in an obsolete space now scheduled for reconstruction. The lonesome illegal, driven to find more of its kind, follows the children in a hazardous journey through the city.
Fumie's younger brother, Akira Hashimoto, recaps the story of the TV series from his perspective as a double-agent, using the ability of his virtual pet Micet. Haraken is accosted by Sosuke Nekome and is warned about investigating further into illegals.
Yasako, attempting to find the place where she first met 4423, meets a boy named Takeru who guides her through the neighborhood. Deducing that the place from her memories was a virtual space deleted by Searchmaton, Yasako heads home as Takeru reports the day's events to a mysterious collaborator.
For their research project, Haraken and Fumie find early records of cyber users who have passed out and reported hallucinations of "the other side". Meanwhile, Yasako spies on Isako as she visits her comatose brother. Deducing that he is 4423, Yasako confronts Isako with her realization that she has met her brother years ago.
Yasako processes the information about obsolete space that she was told by Isako. After hearing what Yasaka has learned, Haraken, tortured by the possibility that Kanna still exists in "the other side", asks Isako to take him there in exchange for Satchii control codes.
Haraken catches a brief glimpse of Kanna before the collapse of Isako's gateway. Fearing for her nephew's life, Tamako Harakawa confiscates his glasses. Meanwhile, obsolete space begins to invade Megabaa's shop as Kyoko, Fumie and Yasako spend the night.
The passage to "the other side" opens at Yasako's house. After Kyoko is taken to the "other side", Yasako and Fumie evade the illegals. With the help of Densuke and Megabaa the girls guide Kyoko's cyber body back to her real body to save her.
With Kanna's glasses, Haraken sneaks out once again to the "other side" where he finally makes amends with a digital apparition of her. Yasako ventures in to the rescue with Isako and Tamako's help. It is revealed that Tamako was the first person to open the gate to the "other side", and the meaning of the show's title, Cyber Coil, is the phenomenon of the separation of one's cyber body from their physical body.
As First and Third elementary merge for classes on the top floor of a Megamass office building, Isako finds herself involved in a conspiracy by Megamass to research obsolete space and the effects of Cyber Coil. Isako is warned off by the mysterious owner of a female Micet.
Yasako and Isako, on the run from Megamass and a powerful new searchmaton, take refuge in Megabaa's store. There, it is discovered that Densuke has the potential to open a stable portal to "the other side", now known as "Coil Domain". It is revealed that Coil Domain, Michiko, Imago and Kirabugs are remnants of an experiment gone awry, covered up by the Megamass conglomerate.
Yasako and Isako is chased by The Black Automaton and after finally evading it searches for a passage to the Coil Domain so they can heal Densuke. Nekome, driven to reveal true nature and history of the cyber technology, tries to convince Isako to join her brother in Coil Domain using Densuke as a portal.
Yasako wakes up in the hospital to find out her glasses was taken away and all the links with Coil Domain have been severed. After the events of last night, all the parents take away the children's glasses. Isako has lost her consciousness, but the truth about the events are being hidden from the public by a Megamass conspiracy. Yasako grieves for Densuke.
Using the glasses that belonged to her deceased grandfather, Yasako travels to the other side to save Isako. However Isako is tricked into hating Yasako and rejects her help. Meanwhile, Megabaa finds out that they were mistaken on who 4423 really is.
Yasako realizes the true nature of Michiko, 4423, and the Coil Domain. Aided by her friends and family she must fight Michiko's grip on Isako and to avoid Nekome's desire to dispose of her consciousness. Isako gets to have her final goodbye with her brother.