Lain Iwakura, a shy, 13-year-old schoolgirl, receives an email from a schoolmate after her suicide. Is it a prank? Lain doesn't feel horror, but curiosity.

Lain receives cryptic messages about existence, God, and a coming prophecy. Meanwhile, Mika's world changes in ways both surreal and hyperreal.

Lain struggles with her identity. Is she a human being, or just a hologram? And are the Knights responsible for the Evil Lain? Lain decides to deal with the Knights once and for all.