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.

Alice, Julie, and Reika are minor celebrities in their class after they witness a shooting at The Cyberia. Lain is given a black-market chip for her computer, but it seems she is also being followed.

Some players of a Wired game called PHANTOMa are dying suspicious deaths. Lain investigates, but her growing interest in the Wired worries her father, as well as classmates Mika and Alice.