People are getting emails from a girl that killed herself last week (Chisa Yomoda), which claim that she only gave up her body, but is actually still alive inside the Wired, and that God is also there. After getting one of these emails, the introverted Lain becomes interested in computers and she ask her father for a new NAVI.
Accela - a designer drug born of nanotechnology - is a big hit with the club kids, but what's that got to do with Lain? Only a madman who painted the dance floor with blood can answer that question - and he's dead.
Lain's friends suspect her involvement in a series of computer errors that caused a lethal traffic accident. Meanwhile, her sister is haunted by mysterious messages demanding that she "fulfill the prophecy".
When an image of herself appears in the clouds, the "real" Lain enters the wired on a search for answers. Her quest leads to a "child-killer" scientist whose devious work is being exploited by the Knights.
Lain risks a meltdown by uploading a Navi clone into her own brain. Later, the border between reality and the wired is threatened when Lain forces the world forget a secret that never should have been revealed.
"God" preaches that our bodies are simply an obstacle preventing the evolution of mankind. An exhausted Lain appears willing to sacrifice her own flesh and blood until Alice convinces her to take a stand against the digitalized deity.