Amidst the events surrounding Tokyo having its traffic information transmission system hacked to cause deliberate accidents, Lain experiences a series of hallucinations that are teaching her (by means of inanimate objects, and eventually her parents) the nature of the Wired, and the supposed almighty god within it. In the meantime, Lain's elder sister, Mika, is driven to the point of insanity due to the Knights repeatedly communicating the message for her to "fulfill the prophecy".