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.

Classmates Alice, Julie, and Reika wonder if that was Lain they saw at the nightclub Cyberia. To find out, they invite Lain to go with them to the club.

A documentary about Roswell gives Lain some valuable information about the pioneers of the WIRED. Later, at the Cyberia, J.J. tells Lain that she left something the day before and hands her an envelop with the Knight's logo on it. The envelop contains a chip. Believing this was the other 'Lain's' doing again, she decides to call Taro's bluff and go on a 'date'. Taking him to her room, Lain demands that he tell her what he knows. Together, with Taro's information and the mysterious chip, Lain finds out more then she expected.

Alone and frightened, Lain immerses herself in the WIRED, processing the events of the past few weeks and searching for the truth of who she is.

Troubled by what she saw, Alice decides to visit Lain at home and find out what is going on. Meanwhile, the two MIB agents receive a terrible shock and Eiri reveals his real motive for removing the barrier between the real world and the WIRED.