Lain receives cryptic messages about existence, God, and a coming prophecy. While she ponders the meaning of this, Mika is about to start a very strange day. While on her way to school, she sees Lain in the middle of traffic. Then, she sees the message "Fulfill the Prophecy" everywhere she turns. As reality distorts around her, Mika rapidly descends into a nightmare that she may not be able to get out of.
Still shaken by the information she received from the Men In Black, Lain discovers that she is being blamed for spreading an ugly rumor in the WIRED. Is what the MIB said is true; is she another person in the WIRED? Or is she doing it herself? Lain must find out or risk losing the one true friend she has.
The events from Cyberia make the girls minor celebrities in their class. But for Lain, more mysterious events continue to occur. She receives a Psyche chip from a mysterious benefactor, strange Men In Black are following her, and it appears there is another 'Lain' on the WIRED.
Toshihiko is captured and tortured by a group of Shokujinki commanded by Yuka's former lover. But soon the Kifūken discovers their location and storm the place.