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In the Case of Kyoko Tohno is the third episode of .hack//Liminality.
After contacting Kyoko Tohno at the end of episode 2, Junichiro Tokuoka travels to the city of Hida-Takayama to meet her. Their meeting is interrupted when Kyoko receives a text message from Helba. After receiving a phone call from a person working under the alias Bith the Black, Tokuoka and Kyoko realize that they are being watched by Helba's agents. A series of messages from Bith lead them to numerous historical sites throughout the city. As several of the messages come from e-mails sent to Mai Minase and Yuki Aihara, Tokuoka suspects that Helba has been following their actions for quite some time.
As they explore the sites, they begin to piece together the story of Emma Wielant the author of the Epitaph of Twilight, each place having some sort of connection to Emma's life. After a chance run in with Kyoko's Father, they discover that he was contacted by Bith as well, working under another alias "Ichiro Sato".
Eventually they encounter Ichiro at a temple. Over lunch he explains that Harald Hoerwick had used the game Fragment, the precursor to The World, to create a tribute to Emma's Epitaph of Twilight. But that alone wouldn't explain the current situation facing The World. He goes on to say that the incidents involving the coma victims were created as a result of Harald attempting to bring the real world into the online world, creating a hazy barrier between the two worlds, a concept called "Liminality". He uses Tomonari as an example. In the real world Tomonari was in Tokyo, in the online world he was adventuring as Sieg within The World. So, where was his real consciousness at the time? The real world or the game world? In order to fix the problems that are occurring, the Liminality must be stopped, and the two worlds must be separated once again.
Ichiro informs Tokuoka and Kyoko that he needs their help, but that in helping him, they will become criminals. Despite the risk, they both agree to help. Ichiro says that CC Corp intends to shut down the servers of The World, thereby destroying any possible clues to awakening the coma victims. He tells them to meet with him on Christmas Eve at Urayasu, then drives away. Tokuoka asks Kyoko if she's really sure about helping him, causing her to reaffirm her commitment to the cause.