The opening song of Serial Experiments Lain starts with a line that you might expect to hear in an argument between lovers or friends who are drifting apart (or just having a bad day): "What did I do wrong?" "Why don't you get it?" "You don't understand me." As the song suggests, two subtexts, (mis)communication and the desire for community, are prominent throughout the series.
Let's start with (mis)communication. The Wired is all about communication. Computers give people a medium through which they can speak... without leaving the comfort of their offices or homes. Kids play computer games with each other over the Wired; people send email to their friends. Despite the positive aspects of this medium, though, Lain shows the downsides. The anonymity of the Wired, though illusory at times (at least, every time Lain walks through the Wired, she's recognized), encourages people to distance themselves from each other. In some cases, such as the rumor of Arisu's forbidden relationship -- attributed to Lain herself -- this lack of clear identity can be used as a weapon. While Lain gains a startling self-confidence (and even spunkiness) by becoming conversant with this digital world and learning to speak her mind, as she delves into her hidden past, she finds that her exploration of the Wired comes with a price.
We also see miscommunication in the characters themselves. Lain in her quiet, self-effacing mode is inept at expressing herself verbally; her body language often reveals her inner tension, but she cannot put that tension into words as readily. Another form of miscommunication occurs when Lain is mistaken for her malevolent "twin" in the Wired. It is not only what is said and how it is said, but who is perceived to say it that has an effect on the listener.
The next question is: why do people want to communicate? The answer is community. Even the lonely hacker hanging out on a discussion group at 3 AM is looking for someone else to talk to. And we've all heard about people who meet and woo and marry online. Even Lain finds a dubious community with Arisu, Reiko, and Juri, and a community in the crowd at Cyberia.
There is a certain poverty in the interactions between characters in Lain. Lain herself has a "father" who only takes interest in her when she works with her Navi, despite his later admission of "love"; her "mother" is indifferent; her "sister" considers her peculiar. Yet even the loss of this faux family is a frightening experience to her. Of her so-called friends, only Arisu seems to care about Lain, and this relationship is threatened by the aforementioned rumor.
Other characters can also be seen in this desperate search for someone to listen to them. Arisu is involved in a relationship with a teacher; Lain's putative sister has a lover, yet there seems to be no deep attachment on either side. Juri and Reiko are conformists who derive comfort from not standing out, and Lain, who stands out in a number of ways, makes them uneasy. Eiri (a.k.a. "God") begs for Lain's love, while the anonymous man with backpack and VR glasses meets his death in trying to impress the Knights. Any attention will do, no matter how inappropriate. Genuine emotion and caring take second place to siren songs of belonging.
The series' cult-paranoia background also lends itself to this interpretation. The Majestic 12 investigated reports of an alien crash -- and the existence of extraterrestrial life implies the existence of a larger community in the deeps of space. Dr. John C. Lilly conducted research on communication with dolphins, (supposedly) another sentient community.
The series is made all the more thought-provoking by the fact that there are such people in the real world (or "present day, present time," if you prefer): people who hold sťances, people who claim to speak to aliens, people who lose themselves in internet personae. Lain is about people so desperate to find belonging, to speak to others who will accept them, that they look to aliens, look to dolphins, look to phantom presences in a computerized otherworld -- but fail to look to each other. Will the characters in Lain ever realize this?
Watch, and wait, and find out.