
In the end, the viewer sees Lain realizing, after much introspection, that she has absolute control over everyone's mind and over reality itself. In the meantime, the anime follows a complex game of hide-and-seek between the 'Knights of the Eastern Calculus', hackers whom Masami claims are 'believers that enable him to be a God in the Wired', and Tachibana General Laboratories, who try to regain control of Protocol Seven. The series sees him trying to convince her through interventions, using the promise of unconditional love, romantic seduction and charm, and even, when all else fails, threats and force.

Masami later explains that Lain is the artifact by which the wall between the virtual and material worlds is to fall, and that he needs her to get to the Wired and 'abandon the flesh', as he did, to achieve his plan. These details are unveiled around the middle of the series, but this is the point where the story of Serial Experiments Lain begins. He then 'uploaded' his own brain, conscience, consciousness, memory, feelings, emotions – his very self – into the Wired and 'died' a few days after, leaving only his physical, living body behind. He had secretly included code of his very own creation to give himself absolute control of the Wired through the wireless system described above. Masami Eiri is introduced as the project director on Protocol Seven (the next-generation Internet protocol in the series' time-frame) for major computer company Tachibana General Laboratories. From this point, Lain is caught up in a series of cryptic and surreal events that see her delving deeper into the mystery of the network in a narrative that explores themes of consciousness, perception, and the nature of reality. Lain finds Chisa telling her that she is not dead, but has merely 'abandoned her physical body and flesh' and is alive deep within the virtual reality-world of the Wired itself, where she has found the almighty and divine 'God'.

But the status-quo of her life becomes upturned by a series of bizarre incidents that start to take place after she learns that girls from her school have received an e-mail from a dead student, Chisa Yomoda, and she pulls out her old computer in order to check for the same message. Lain lives with her middle-class family, which consists of her inexpressive older sister Mika, her emotionally distant mother, and her computer-obsessed father while Lain herself is somewhat awkward, introverted, and socially isolated from most of her school peers. The series focuses on Lain Iwakura, an adolescentmiddle school girl living in suburban Japan, and her introduction to the Wired, a global communications network which is similar to the Internet.
