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.

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.

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.