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In Tsuruki City, a security company representative named Takahagi Koudai plays a zombie shooter in his apartment, becoming unnerved when his character unlocks a door in the game that they shouldn't have been able to yet. At work the next day, Koudai gets into a conversation with a coworker named Kayama Atsuki, the two discussing the strange happenstance in the game. Koudai later receives a mysterious e-mail from a sender marked "M", claiming that something would happen a week after Tanabata and on Tanabata itself.
A week later, on Tanabata, when Koudai goes to work he finds that none of the company's security systems are working, including their own, and that the phones aren't working either. As no calls or e-mails are getting through to the company headquarters, Koudai's boss, Shinichi, sends him to headquarters to check things out. He's subsequently stopped in traffic by a car accident. While there, he runs into his friend Mekage Mika, a traffic officer. He learns from her that an invisible barrier is impeding all entry and exit from the city. Deciding to go back to the office, Koudai goes back to his car, only to find that his car door lock has also stopped working.
The next morning in Tsuruki High School, Koudai's little sister Otoha heads to the music room to open it and finds it already open, assuming it related to the "unlocking incident" of the day previous. Inside, she finds her classmate Shihogi Kanoe dead, torn to pieces. Stricken, Otoha informs her teacher Nonomiya, who has also seen the body and called the police. The two discuss what could have killed her, Otoha thinking it might have been a bear. The book flashes back to a bear escaping from the Tsuruki City Zoo when the door to his cage was unlocked. Deciding never to return to the cage, the bear heads forth, having realized a new "ability" he can use to hunt.
Meanwhile, Koudai faces continual calls at work from customers panicking over their systems and locks failing. He soon learns from Atsuki that a girl had been killed at the school, although thankfully not his sister. He learns a convict named Saruta also recently escaped, and was spotted near the zoo, where several animals have also been escaping. Returning to work, Koudai receives another e-mail from "M" claiming that Tsuruki City is now under the control of the "Master". He responds to the e-mail and elects to tell Shinichi about it. Later, two days since the incident began, Otoha and her classmates discuss the "unlocking" strangeness before they're startled by a shape at the window.
Later Mika and her partner, Takatomi, drive back to the station in their patrol car. Receiving a radio call that Saruta was spotted near the high school, they drive there and find him surrounded by onlookers, brutally killed. Four days since the incident started, Shinichi has gone missing and Koudai ends up consulting with Atsuki instead, who determines they should stop the culprit before a week had passed. With no leads, the two argue about whether or not to bring this information to the police, Atsuki convincing Koudai not to for now. They drive to Atsuki's apartment, and Atsuki uses his computer to hack the company system and determine the e-mail was sent from an internet cafe.
On the way to the internet cafe, the two stop at Tsuruki High School and encounter Mika, who warns them to stay back. Koudai's father, Heiji, then arrives; while Atsuki heads to the internet cafe, he takes Koudai to a nearby coffee shop and explains that a barrier surrounds the high school like the one surrounding the city. He also explains that Saruta was killed by the bear that escaped the zoo, which had killed Kanoe previously. With even tranquilizer guns no longer working, the bear entered the high school and the barrier went up afterwards.
Worried about his sister, Koudai joins Atsuki in trying to find the culprit behind the barriers. He tries to start his car, only to find it doesn't work because a key has to be inserted into the engine; he deduces that the unlocking phenomenon is getting stronger. Meanwhile, Otoha stays with Mizuki while reflecting on the situation, with the bear attacking the students and teachers in the school. The bear enters the room. Later Koudai awakens from a dream about Otoha in the early morning and finds a bunny she made for him in elementary school, attaching it to his cellphone.
At work the next day, Koudai meets up with Atsuki, who promises to share with him what he learned at the cafe when they're alone. The two talk further, and then decide to head to Atsuki's house. During this, Otoha and the other students still struggle to escape and to survive the bear; Otoha and Mizuki are hiding with Nonomiya and some other students in the music room, although they leave for a time and discover the invisible barrier keeping them trapped. After an hour's walk, Koudai and Atsuki arrive at the latter's apartment and check the internet cafe's security footage, discovering that Mika sent the e-mails. After discussing this revelation, Atsuki checks through her internet history while Koudai goes to the high school to talk to her directly.
When Otoha and Mizuki return to the music room, they find Nonomiya gone to find the other staff. Otoha then overhears three troublemakers, Seiryuu Kouji and his friends, discussing the invisible wall, Kouji suggesting it to be the result of a curse. When Koudai arrives at the high school he meets with his father, and they learn from Takatomi that Mika is at home, receiving a visit from Shinichi. Meanwhile, Otoha and her classmates learn that Nonomiya has been killed by the bear. Back outside, Koudai is summoned to the library by Atsuki, and Atsuki shows Koudai a book on Tsuruki City's history that Mika checked out.
The book tells of an incident in the Meiji period where all the locks stopped working; this was allegedly a curse wrought by a girl named Kameko, who made an offering to the gods using a black box in the city's Mekage Shrine. Koudai and Atsuki visit the shrine in search of Mika; once there, they find Shinichi and spy on his meeting with Mika inside the shrine. They learn that Mika was ordered by an e-mail to offer her personal effects to the shrine and that this caused the locks to stop working, although she was unaware this would happen and appears ignorant when Shinichi asks her if she was ordered by "Evillious.net" or "Allen" to do it. Shinichi then stabs Mika, claiming it would let him win the "game"; Koudai disarms Shinichi and calls for an ambulance and the police.
In the school that night, Otoha and Mizuki go to the bathroom together and encounter Seiryuu and his friends; they're forced to flee when the bear arrives and kills one of Seiryuu's friends. Five days since Tanabata, Koudai heads back to Mekage Shrine. Otoha, meanwhile, heads out of the music room to find Seiryuu, who also left. After finding him making plans to kill the bear, the two enter into a confrontation with the animal itself, and Otoha narrowly escapes with Seiryuu's help. In Mekage Shrine, Koudai places the bunny Otoha made for him into the shrine's black box as an offering.
Finding it to have seemingly no result, Koudai leaves. In the high school, Otoha and Seiryuu take refuge in a bathroom stall; at that moment, Otoha receives the bear's abilities to alter locks and create invisible walls. Later, Koudai returns to his childhood home and meets with his mother. He watches the news, with reports on how everything has returned to normal since the bear was put down. Otoha was previously able to bring down the barrier and fix the guns and cars, allowing the students to escape and the bear to be captured. Koudai realizes that the bear must have been the "master" mentioned in the e-mail, as Mika's offering had been a bear phone strap, and that his offering had given Otoha her powers.
Later Allen, the head of Evillious.net, e-mails to all its members a summary of how the "game" had played out. The summary reveals that Mika was the "Starter" of the game, and that Shinichi is disqualified for killing her instead of the "Master". It also reveals, among other things, that Seiryuu and Saruta were involved in the "game", and that Atsuki, the "winner", was as well. Evillious.net plans for their next game to be even more thrilling.
- The events of Unlock City are alluded to in the epilogue of Deadly Sins of Evil: Master of the Heavenly Yard, with the the SNS "Evillious" chat members discussing an article about a bear escaping in Tsuruki City.
- It is unknown if "Evillious.net" bears relation to the SNS "Evillious" chatroom; similarly, it is unknown if "Allen" bears relation to Allen Avadonia of the Evillious Chronicles.