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It was all aliens!.
Everything in this series has been the work of Aliens.

The Wired was created using alien technology, it is like the internet but it has the power to tap into the human mind, and the collective unconscious shared by all life forms that produce brain waves. The Wired is not an actual location; it is merely the network through which certain beings can access this unconscious.

Humans do not have the capability to consciously access this shared unconscious; their brains are not developed enough. It requires a creature that has already mastered the powers of the mind: The Greys.

Lain herself is a young grey, which is how she is able to manipulate so much through the Wired. Though she is unaware of her status as an extra terrestrial she slowly learns just how much she can affect the real world just by changing memories and altering perception through this unconscious.

Unfortunately because Lain is not fully developed or aware of her heritage she was unable to stop the collective consciousness of the human race from affecting her mind: fracturing it. All of the other Lains are different versions of the originals psyche. As are Chisa and Eiri; whom did die but the echoes of their consciousness still remained in the collective unconscious which influenced Lain’s creation of the mental constructs in her psyche.

The grey Lain saw in her doorway was actually the part of her psyche that had become aware of what she really was-Lain has its body when she is speaking to Alice from her doorway.

The Emails from Chisa were not from her at all. They were from Lain’s real family, in order to get Lain interested in the Wired so she could begin to unlock her true potential. The Emails were also sent to her other classmates in case she never bothered to check her own.The greys also were the ones who kept sending Lain parts to upgrade her Navi so she could further access the Wired, until it would come to a point where she wouldn’t even need a machine to affect the collective unconscious.

Lain’s ‘parents’ are indeed aware of her origin, they have no choice but to obey the task that the greys have ordered of them. Mika’s behavior change was also caused by the greys, she was unaware of what Lain really was, but she was getting too suspicious, so they abducted her and either brainwashed, or replaced her.

The greys are the ones that killed the two men in black near the end of the series. They didn’t want them looking any further into what Lain was.

Eiri’s attempted manifestation was actually Lain's own telekinetic powers activating, though through the psyche of Eiri.Finally, Lain has realized just how powerful she is and uses an ability almost unheard of for even her people: Chronokinesis. She turns back the clock and reverses everything she has done with her powers, and makes a few changes; including removing herself from the equation.

At the end Lain still exists, she still has a body. But nobody can perceive her. A grey comes to her in the guise of her false father-perhaps her real father-and gets rid of her split psyches. It is revealed to Lain what she is and why she was placed on earth with a human family in the first place: To help humans prepare to join the intergalactic order. However it is decided that humanity is not ready.

Lain returns to her home with her real family, but is happy to drop in back on earth every once in a while.

There! Happy Ending!

Eiri's work is based off that of Nikola Tesla.
It was Tesla who first envisioned a wireless system that harnesses the entire world's electromagnetic field to encompass the entire world, serving as both a power source and an omnipresent super-Internet. Eiri simply modified Tesla's system to be able to compatible with human neurons, unifying them into a single collective subconscious.

Also, based off the theories of Nikola Tesla, the "wired" may actually be scientifically plausible.
If you were intrigued by the ideas in SEL and wonder if some of the ideas presented within the show are actually practical, watching the minute between 13:45 and 14:45 on this video may give you goosebumps.

Lain is, purely and simply, developing increasingly severe symptoms of paranoid schizophrenia throughout the series, and spends much of it confined for her own sake. Everyone's reactions to her are just as normal as real life, but are all filtered through Lain's hallucinations and delusions.

From her fingers smoking in episode one to having "stories" told to her by apparitions of her parents to the Men In Black watching her, all while having vastly distorted perceptions in her everyday life and a totally insensible idea of reality. She hallucinates almost constantly, has theistic, paranoid delusions—including delusions of reference—and expresses bizarre and inexplicable behavior, such as being seemingly emotionally unaffected by a manic and disturbed man with a gun as he kills two people, aims it at Lain, and then himself, during which Lain responds by ignoring Alice's pleads for the both of them to get to safety, and then putting herself in further danger by approaching him without any regard for the reality of the situation. Nonexistent, flattened, or otherwise grossly inappropriate emotional response and behavior to a charged situation is common in schizophrenia.

Her "room" that mysteriously becomes a massive hub of safety for her consciousness is not real, and is highly likely a place in which she is confined to be treated for being unable to participate in everyday life. Her mother, father, and sister have no idea what to do with her, and they become frightened of her. She literally argues with herself with a misperception of a "part of her", as she says, that she doesn't want. She believes she is the center of the entire world, and everything refers back to her, hence her delusions of reference.

When Lain's father visits her in her place of confinement, he does what most people do in such a scenario—he tries to talk her out of her delusions using her own logic, but without success. Her mother simply ignores it completely in order to cope. Her sister, Mika, also has a great deal of difficulty coping with Lain—not just because of Lain's condition itself, but also because of how distressing it is to see her like she is, something with which she has no experience and can't understand why her sister is acting the way she is. When Lain sees her sister muttering to herself in the hallway, it is almost literal: Her sister simply has no idea what to say to her every time they're together, and naturally worries that she, too, might also be affected by the illness, as is common in siblings in which one is seriously mentally ill.

In episodes 12 and 13, Alice visits the place in which she is confined, whether it's her own room or a psychiatric hospital room—but to Lain, she is merely visiting her in the reality she's created for herself after her symptoms have fully manifested. Alice is speaking the truth about her not attending school, but Lain misinterprets this to fit her perceptions of what reality is. While Alice talks to her, she is at a loss for words, and Lain is making no sense. Alice tries to bring her back to reality, but Lain hallucinates Masami Eri's voice, and then begins to argue with him out loud. What follows scares Alice into hysteria, but she's actually frightened of Lain, not the imaginary Masami Eri that Lain has created herself. Hence, when Eri disappears, she is still hysterical, and tries to push Lain away while screaming for her to get away, scratching her in the process.

Basically, there is nothing supernatural actually happening at all. Lain simply begins to experience some of the most severe symptoms of schizophrenia, with extremely vivid hallucinations and delusions of the outside world, one in which she is never actually a part.

Alternate Technology History
The computers are called Navis because it's short for Knowledge NAVIgator—you can see a little animation of this in episode ten, if I recall.

"Knowledge Navigator" is an imaginary class of computer that (former Apple CEO) John Sculley wrote a book about. The concept has informed a lot of what Apple has done with the iPad, and the computers in Serial Experiments Lain seem to act a lot like these.

The computer corporation is called "tachibana" which is a type of orange, just to avoid trademark issues with Apple.

So in the Lain 'verse, Apple is all computers.

This might help to explain why Lain, a virtual entity with supposedly rather indirect control over the physical world (if Masami Eiri is to be believed), might nonetheless be able to pull off a Ret-Gone: she has a posse. The Cult of Apple is a literal cult in the Lain 'verse. (Maybe the same people as the Knights? Anyway, point is they will do what she says.) They don't have much resource to work with under normal circumstances, but in the modern world most money exists as numbers in databases, and that's exactly the sort of thing Lain would have been able to acquire.

So she actually just paid someone else to "erase" her from history. This might not even be that hard given the curious effects that Accella has on people. The poor guy who takes it in episode two is able to look at Lain and immediately know exactly who she is—because Accella patches him into the Wired, and without the need for the enormous intrusive interface that Lain sets up in her room. It may not be very good access to the Wired, but that elementary ability to put thoughts in people's heads could be very handy if you need, e.g., to brainwash someone into thinking they are actually the same Chisa Yomoda who committed suicide last year.

Lain is the manifestation of our collective subconscious
Lain is the manifestation of our collective subconscious. She's fragmented into different aspects of ourselves that we suppress: there's the child-like Lain, the bold Lain, the evil Lain, and others. Certain engineers tuned the protocols and hardware running the Wired so that it would allow information to cross to and from our collective subconscious, which had the effect of allowing the waiting Lain/collective unconscious to form a more conscious entity. Masami Eiri's goal was the reverse: to infiltrate the collective unconscious from the Wired.

Meanwhile, the child-like Lain desired a family so she created one, the bold Lain hung around Cyberia and had fun, and the evil Lain spied on people to learn their secrets. The child-like Lain saw the pain that she (in her various forms) was causing Arisu, and decided that humanity's collective unconscious should not have such reckless power. So she rewrote history and altered the protocol so that it can't interface with humanity's collective unconscious.

At the end of the series, it's implied that Lain has killed a lot of people — definitely the two Men in Black, probably all of the Knights, and possibly a large number of people; it's only certain that she didn't kill Arisu. The KIDS experiment, years earlier, caused the exact same thing to happen: it empowered a collective unconscious on a much smaller scale, whose various incarnations ran amok and killed all the test subjects.

And therefore, millenia ago on a distant planet...

The same thing killed the Krell in Forbidden Planet
Just like a collective subconscious killed the KIDS subjects, the Krell built a Wired and their collective unconscious wiped them all out. The just had much more powerful psi amplifiers than we did.

The same thing killed / instrumentalized all of humanity in Neon Genesis Evangelion
This theory was inspired by the similarity of Freudian (which influenced Neon Genesis Evangelion) and Jungian (which influenced Serial Experiments Lain) theories of psychoanalysis. In fact, Jung himself was influenced by Freud. How did it take place, anyway? In the world of Eva, the collective unconscious was personified in the form of Adam and the Angels, which humanity / the Lilim are trying to repress (lampshaded by the Angels' Mind Rape abilities, and the canonical fact that the Angels are the alternate evolutions of Humanity). Seele's real intention was to create the Wired, and alter it so that the collective unconscious can be manifested into a conscious entity where humanity can deal with them physically. Basically, a huge ritual of psychoanalysis. Gendo is Eiri, both wanting the physical man to penetrate the collective subconscious, causing the death of all humanity just like the KIDS Experiment.

After Lain Ret Conned herself out of existence, the world of Code Geass takes place
Charles was trying to replicate what Eiri wanted, to take control of the collective unconscious. C.C. and Lain are also the same entity.

The Wired, is in fact, TV Tropes Wiki.
The Wired is a hive mind made through connecting humanity's psychic powers via the Internet. Wait, how come the connection of humans create a Deus Est Machina? In other fiction, beings wired together (for example, the Borg) don't produce an instant Deus Est Machina. Where is the real Deus Est Machina, then? Answer: TV Tropes Wiki. Think about it: Tropes transcend reality. Enough tropes can either ruin your life or strip a human away of your Fourth Wall. Enough humans without a Fourth Wall could outsmart, or even transcend and manipulate, reality. Enough humans with enough tropes to transcend reality can make a God.

Eiri knew, that the simple wiring of humans, will just make them too cold and rational to prevent creation of a God. After all, machines are built to be logical. Too much irrationality (for example, Religion), will prevent humans from merging with the Wired, and too much rationality will prevent the existence of Gods. To allow this, he broke down the cold rationality that is so characteristic of the Internet through the Tropes, which are irrational enough to break the Fourth Wall yet logical enough to allow existence with the Wired.

Lain is a bank account cracker.
By the end of the series, Lain has somehow crammed an entire network site on her bedroom, complete with 19 inch racks, professional-grade switches and routers that must very likely support advanced stuff like port aggregation, Spanning Tree, linkstate routing, DHCP and whatnot, maybe 4 servers, 3 computers, most likely a super-fast Internet connection plugged directly to the carrier, and on top of that, she even has a neural interface on her computer. Although her site is rather small compared to an university network site, it's still really huge, and chances are it would cost like 70,000 dollars!

Therefore, in order to fund her purchases, Lain works as a freelance hacker and secretly steals money from bank accounts. As a result, the authorities eventually found her and figured out who she was — which is why The Men in Black are always stalking her outside of her house.

  • Didn't her overlooker/adoptive dad buy her all that stuff?
    • He just bought her the top of the line, but otherwise ordinary Navi. After Lain found the Psyche-processor and installed it, the rest of the stuff grew around it like vines. See how the machinery breaks through the house's wall in the later episodes, and how new wires spontaneously attach themselves to the house to provide electricity for it all. Serial Experiments Lain isn't science fiction, but Magical Realism.
      • Given the fact that Lain is god, her family is part of a secret orginization, another (possibly the same) orginization worships her as god, a demi-god looks over her, and she has superhuman/strange powers and a split personality, money was probably not an issue. She probably didn't even buy it, and instead it was delivered/was installed/just appeared out of the blue. The Psyche chip just showed up in her locker, and other things were left for her at Cyberia, so we know she was being fed equipment.
      • Futher, it could have been Eiri that was organizing her reception of all this in order to draw her closer to him and cut off her connections to the physical reality.
      • I always assumed the stuff left for her at Cyberia was from the mostly-independent Lain of the Wired, or something. The details are pretty much moot, however, the important part being that there's a couple of ways it could have happened, and it did happen.

Masami Eiri is actually the good guy, and most of the plot is the result of a huge Gambit Roulette by him
If I was going to use spoiler-tags, I'd have to cover the whole thing with them; but seriously, why are you looking at the Wild Mass Guessing page if you haven't already watched the show? All the same, Here there be spoilers. ARRR!

God/Masami Eiri wasn't the one who gave Lain a body; Lain of the Wired did it herself, as part of a ploy to become God of the real world and the Wired. In essence, Evil Lain is the real Lain of the Wired, and, already omnipresent and omnipotent within the confines of the Wired, created Real Lain in order to break down the barrier and complete her apotheosis. Eiri used Protocol 7 to upload his consciousness in order to stop her from accomplishing this, teaching her by example that no one should wield that kind of power. By accomplishing his own pseudo-apotheosis, Eiri is able to figure out the details of her plan, and generally engineer things so that Real Lain subsumes her Wired counterpart, and reverses the plan already set in motion by resetting reality to just before the point where she became Real, at which point the new dominant Lain chose not to create herself and to remain as a distributed presence in the Wired.

Arisu/Alice is the hinge on which this all turns. Lain of the Wired was simultaneously completely connected in terms of information, yet completely disconnected in terms of emotion and human interaction. Eiri, using his vast reach as God, engineered events so that Lain would come to have a true friend, and her final decision to execute the all-reset was catalyzed by her genuine love for Arisu. The Power of Love was enough for this Lain to overpower the other Lains, and as the new dominant personality she used her power to undo the general badness her original self had set into motion. Furthermore, by learning that it's best to just watch and only occasionally (and subtly) intervene, I propose that Lain went on to become God from Futurama as well. Hey, why not?

Finally, Eiri did all this knowing that Lain was going to ultimately hit the master reset, and that he himself wouldn't die. It's like the ending to Donnie Darko, only weirder and more ambiguous. Now there's a sentence I never thought I'd compose.

  • You... actually understood what the heck was going on?!
  • My God...the series actually makes sense now.
  • Thank you for helping to clarify this for me. However, Eiri's behaviour in episode 11, when Arisu/Alice finally goes to lain's house. His freak out over Lain's decision doesn't strike me as particularly heroic, especially if he knew that her meddling would wipe him out of existence. Still, it's good to keep your points in mind; they're by far the most coherent explanation I've yet to get about this series.
  • Interesting interpretation, but still not without problems, if taken as a viable theory for what the hell is going on, rather than simple WMG. Namely, that Lain of the Wired isn't evil - she is just Lain's assertive, bold side, free from the social repression. The crazy Lain is yet another personality, and possibly not a true reflection of Lain at all, but a creation of the collective perception of Lain in the Wired: a creepy urban legend come to life.

Serial Experiments Lain is a sequel to Haruhi Suzumiya and Lain is Haruhi

The events of the series occur after Haruhi realizes she's essentially God and rewrites reality- it's why it takes place in the present day...present time HA HA HA HA yet technology is more akin to Twenty Minutes Into The Future.

  • Or vice-versa?
  • If Lain is Haruhi, then the Wired is the Integrated Data Thought Entity, and Yuki works for Eiri.
  • Lain does look like a cross between Haruhi and Yuki....

Haruhi Suzumiya is a sequel to Serial Experiments Lain and Haruhi is Lain

I think this makes more sense than the reverse. At the end, Lain is lonely. To alleviate her loneliness (years spent observing humanity without interacting) she wills herself into human form and suppresses her powers and memories. Two caveats:

  • All versions of Lain/Haruhi are present: the child Lain (distant and bored), the bold Lain (creates the club), and the evil Lain (gets a computer)
  • She only shut of conscious access to her powers, her subconscious can access her powers

Lucifer is a sequel to Serial Experiments Lain
  • Specifically, the series is called Serial Experiments Lain. The "Lain" Series is a series of replacement/artificial gods created by a group of Mad Scientists. First came the prototype, Laine, then A-Laine then B-Laine, all the way up to E-Laine from Lucifer. The character in Lucifer is called Elaine, but it's only because nobody but God realized that she's actually the fifth model among the functional Laines.

The "reset" chronology is that of our world.
Not too wild, I think — my idea is that Lain does take place in the "present day, present time" but in an alternate chronology where technology happened to have developed a little earlier due to Lain's influence. Once Lain removes herself from the timeline, the world is our world.
  • The only problem with this is that they still have the strange cell-phones. Which is why they need to digitally edit all of them out after the reset. Because that would make the
series 100000000000000x creepier.

... from a Gnostic perspective.Basically, the information in the Wired amalgamated into a benevolent Godlike entity. The entity is the "Lain" who is said to have always existed in the Wired. The God decided that in order to guide humanity, it needed a human perspective. It thus directed events to create a human-Wired interface, and the creation of an Artificial Human, all for the purposes of creating Lain. It set events in motion to ensure that Lain is eventually brought back to the Wired, learning much about herself as a human and humanity in general in the process, all for the purpose of reuniting Lain with God. Masami Eiri was directed to being a god for the purpose of teaching and guiding Lain (and acting as a Demiurge figure).

Lain is the first Digimon
Serial Experiments Lain and Digimon Tamers were both written by Chiaki J. Konaka. In Tamers, Digimon were artificial life programs that evolved within the Digital World, a parallel reality within Cyberspace. They developed the ability to "bio-emerge," manifesting as physical beings by synthesizing artificial proteins — much like the way Lain's physical form was created using "artificial ribosomes" and the way Eiri attempted to manifest physically in the climax. The barriers between reality and the Digital World seem to be eroding, since there are portals that allow passage between the two realities.

Perhaps the world Lain created at the end of the series is the world of Digimon Tamers. Even though she removed herself from people's perception, the divine force/Jungian collective unconscious that she symbolizes is still present, as are the Schumann resonances that can tap into latent human psi abilities and bring about seemingly supernatural events. These psi abilities are strongest in children, which is why children have a special bond with Digimon. Somehow the Digimon artificial life programs, as they evolved, must have found a way to tap into these latent powers and thereby gain access to the real world. The Digital World is a name given to the domain within the Wired where the Digimon programs reside, or perhaps the Wired goes by a different name in this time/reality. Maybe the catalyzing force of digivolution that became Calumon (the non-evolving Digimon who enables other Digimon to digivolve) was created by Lain to counteract the destructive force of the D-Reaper, or is an aspect of Lain herself.

  • One puzzle is that both realities have a Juri Kato, but the two characters are different. The Juri of Lain is a gregarious teenager with frizzy hair, while the Juri (Jeri in the English dub) of Tamers is a shy, straight-haired preteen who looks a bit like Lain (and is dubbed by the same actress in the English version). Of course, Kato is a common name and Juri, while not ubiquitous, is a valid given name in Japan, so it could simply be coincidence.

Lain offed herself, and was reborn as Rakka
Lain was a lonely, reclusive, insecure and confused girl who thought nobody would notice her disappearance — except for Alice, who was her only friend and stayed with her until the very last moment, even when finally confronting Masami Eiri. Despite this, she deleted herself from existence anyway. Lonely and without anyone to confide her secrets even after wiping her memory from everyone in the world, she offed herself. Since she killed herself, her presence in the Wired was no more, and thus she had essentially disappeared from the world. To redeem her soul from the sin of hurting Alice, she was reborn as a haibane — as Rakka, that is.

Evidence supporting this claim is the fact that Lain looks like Rakka without wings and with shorter hair, and the fact that Yoshitoshi ABe was behind both productions.

  • This troper would like to point out that ABe being behind both productions pretty much explains why Lain looks like Rakka. Hell, look at some of the art for Welcome to the NHK (the specific example I can think of is the novel's cover art, which is on the series' Wikipedia page), in which Misaki also looks very much like Lain. Either ABe is fond of drawing girls who look similar to Lain, or that's just the way he draws all his female leads, or both.
    • This is Wild Mass Guessing, however.
    • ABe can't really be considered as being "behind" both production. He conceived of and wrote Haibane Renmei, so it's definitely his. But Serial Experiments Lain was written by Chiaki Konaka. ABe was only brought in to the production after Ueda saw his artwork online. He did character designs and backgrounds, but that's it. If you look at the other teen female characters he's done, you'll see that they've all got similarities. He tends not to do the blue or pink hair and so forth, so this isn't too surprising.
  • This troper thinks it makes more sense if it was Chisa who became Rakka, since Chisa jumped off a building to her death and Rakka fell from the sky in her cocoon dream. In which case Lain is actually the crow, and Reki may well be the girl who jumps in front of the train in episode 1.

This is the same world in which Paranoia Agent is set.
W Hy, pray tell? It has everything to do with the dead people. In episode 8 of Paranoia Agent, a group of people agree to commit suicide together as part of a pact they made online. At the end of the episode, we get a bit of a Tomato in the Mirror effect - they're already dead. Given how death works in the Wired of Lain's world, this should make sense.

Lain is Teddie in an alternate reality.
They both were born from their respective media, both of them were able to manifest in the real world, and the bear motif they share.

Lain is a tsukumogami of the modern era.
Bear with me folks, this is WMG. A tsukumogami is an object that inexplicably comes to life after it exists for a hundred years. The internet hasn't been around that long, obviously, but with so many people using it, the process may just be speeded up. Oftentimes in anime, tsukumogami create a human avatar, so there you go.

Lain is Shinji reincarnated.
Because somebody had to make this assumption soon enough.

Lain is an alternate universe minus.
They look similar, they have weird names, they both have few friends, there's the whole God thing and there's the whole weird things happening via them. Just in this universe, she's an Emotionless Girl in a Darker and Edgier world, and everything is more warped and strange. Though, I haven't really gone further than this part of the theory.

Both are based off Cyber-Magical Realism. And Lain might be the One of that time.....

Except the Soul-Collecting Reis were turned into Soul-Collecting Lains.
  • Lain can also be Shinji Ikari, since both were given control over Instrumentality.

Serial Experiments Lain happens in Real Life, Present Day, Present Time!
  • Let me explain. The anime gives references to the Internet, the Schumann Resonance (Earth's electromagnetic field) and man's ability to produce psychic power when wired together. Over time, as we are getting more and more addicted to technology, it influences the nature of Earth (from green nature utopia to a wired Crapsack World), so somehow we are either just complete jerks worshipping cyberspace, or somehow our psychic powers are being harnessed by cyberspace, giving it the ability to influence the world. The best example would be TV Tropes itself, which has the power to influence fiction even though it is just a wiki with over-the-top theories.
    • If SEL was real, then there would be the Eldritch Abomination that is Lain Iwakura, who is watching us masturbate.
      • Lain isn't real, since the Wired of Real Life is still too weak to invade human privacy directly (the internet still feeds on second-hand psionic power, NOT from living souls, and there's the problem about China). Cyberspace can influence matter and events, but not man's power of free will (unless somebody hacked China's great firewall and acquired massive psychic potential from the most populous people on earth....).
      • Cyberspace (Wired) doesn't just lack the ability to limit free will, in fact it gives man too much free will......
      • That would be a perfect example of limiting human free will. That multiple people assume the same behaviour-pattern out of perceived sense of anonymity is a demonstration of how the loss of self-identity can cause people to act more like a Jerkass collective than individuals in control of themselves.

SEL takes place in the same world as The World Ends With You.

  • Layer 5 is particularly full of parallels. "God" sounds like the Composer. The "prophecy" written in red ink is talking about the Game. The weird ghost people Lain keeps seeing are Players. The person who got run over in Shibuya was Shiki, and she ended up in the Game (as did Chisa and the girl who got run over by a train in the first episode). Hell, maybe Mika actually died in this episode and gave her sanity as an entry fee into the Game, which she lost, but she was then returned to reality after the end of TWEWY.
    • Also, Imprinting is a technique derived from the Wired, and JJ is actually BJ, who actually shows part of his face when he's off-duty. He met the other Def Märch guys in Cyberia.
    • Any which way, Lain ends up either a Composer or even a full-fledged Angel, and Joshua hates her.

Doctor Who is what happens when Lain gets bored.

It explains a lot... the inside of the TARDIS is inside the Wired. It doesn't really time travel, that's just Lain continually resetting the world. And Lain is all of the Time Lords; each version of the Doctor is just Lain through the eyes of the current companion. And she's the Daleks. All of them. And every other recurring character with the possible exception of the various companions... the Master, for example, is Evil Lain...

  • More seriously, Lain's world is part of the Divergent Universe, which is why she is able to partially reset it. Masami Eiri is actually just one of Rassilon's regenerations, trying to take power from within the Divergent Universe to become all-powerful.

Lain is in fact, Ceiling Cat, or some other Lolcat
The proof: Evil Lain actually watched Arisu masturbate.

The WMG: The real Big Bad of the entire plot isn't Eiri, but Anonymous, being the dominant I Am Legion entity that he is. Lain might be the collective anthropomorphic manifestation of Anonymous' own creation, the Lolcats. Obviously, Lain, who actually watched Arisu masturbate and is also the God of the Wired, is Ceiling Cat. In the SEL Universe, Eiri is a member of Anonymous. Consumed by the power of the G.I.F.T, he tried to use both his psychological knowledge of the collective unconscious and his knowledge with computers to access the collective unconscious and personify it into Lain / Ceiling Cat. Through Lain / Ceiling Cat, they will preach the message of anonymity, and maketh anonymous disciples of all nations. However, Lain sacrificed herself to forgive our sins and prevent the awakening of Anonymous from the nether abyss. If Eiri and Anonymous succeeded, however, through the collective unconscious Eiri will awaken Anonymous from his abyssal slumber as a group of anonymous kids over 4chan into an actual Legion of Demonic Invaders from Hell who will purge the world with fire, brimstone and endless memes and can only be identified and expected through this quote: I Am Legion, For We Are, Many........

Most of the entire series is a hallucination by Chisa Yomoda
Chisa Yomoda encountered Lain, who was never real in the real world, while she was in the Wired. Lain teased her to near-suicide. Chisa then hallucinated what would happen if she commited suicide and if Lain was real, but decided not to go through with it. She then went back into the wired after school the next day, encountered Lain, and gave her a stern talking to. She also said that the real world is better than the Wired, so Lain decided to come to the real world and see for herself

Deus Ex Machina - Your literal God From The Machine
This is less of a WMG than it is a hypothetical elaboration. However, it has both insanity and a mass of words, so I'm putting it here.

Warning: what follows is... a somewhat solid text wall, complete with punctuation, far too many brackets, and a wanton abuse of the word "reality" for mortar. Please ignore at your own discretion.

Lain's presence was a bridging that allowed the superimposition of the Wired over Reality, breaking down of the barriers between the human mind and, essentially, a dispersed neurological interface on a macroscopic level, defined by the flow of information (as is the human mind). When those walls broke down, it allowed individual minds to impose their subjective reality (defined by their identity) onto the subjective realities of others, creating realities that deferred from the objective norm while subverting the associated interfacing flow of information to project it to a different end than what would have originally occurred without the interference. "God is in the Wired" is the idea that a persistent and large enough influence over the flow of information that composes the macroscopic network, will cause it to change in flow, and hence change the nature of the interfaces of those involved/linked to the network, influencing the aforementioned sentient entity on the receiving end. Hence, with the same conditions, if one individual can project a persistent subjective reality, e.g. "I, [Insert Name Here] am God", then eventually, through the superimposition of realities upon one another and their constant two-way pooling (i.e. information is both given and received simultaneously without a filter or seive (such as a barrier) to contain or regulate the interaction), individuals will come to believe that the original perpetrator, [Insert Name Here], of the idea/information is in fact a God (because all subjective reality has been re-defined/influenced to that end. Now in normal circumstances, if something caused a group of people to believe that someone else was a religious figure etc., it wouldn't have the ability to impact upon what you could call "physical" reality. However as we saw with the KIDS experiment, the psychic power inherent in transmission of electrical impulses (as in information) within the brain can achieve a change in physical reality through the release/transformation of that energy. In a reality where the borders between the Wired and Reality are lost, the transmission of information becomes a dominant overlay superimposed onto physical quantities (with both microscopic and macroscopic neurologics/networks combining), such that when there is no barrier between the Wired and Reality, manipulation of physical matter becomes subject to the influence/control of the transfer of information (now become an open application of energy upon the state of matter at a nuclear level). (As to this last part, you can take either the idea that: the mass energy in information transfer, in both the human brain and in the network of the Wired, is applied to matter by the driving force applied by said energy, configuring matter into a state constant with the configuration of the energy-flux of information-interchange; or use the philosophical cross theoretical physics idea that because an objective is determined by consensus and hence, as, according to a very simplified version of Shroedinger's Cat with the Copenhagen interpretation of Quantum Mechanics, in that: the universe consists of infinitely possible quanta in the infinite probabilities of an event occurring as determined by quantum waveform, - however when we measure or observe a definite aspect of quanta and to evaluate it in discrete form, this causes wavefunction collapse where the probabilities of any other form for the quanta fall to zero, and the quanta is defined by the aspect observed (i.e. there are multitudes of probabilities until a definite action is observed/measured, at which point the wavefunction is reduced to one single eigenstate), - and hence if a pervasive reality is determined to be observed via consensus, you could probably bastardize this idea to the conclusion that waveform collapse occurs as all possibilities are reduced to 0 upon the defining measurement of a perceptive reality, but I don't know if that isn't bending the rules just a little too much).

As a result, Lain originates from the Wired, its Avatar/goddess pulled into being by the development of the Wired into manifest sentience. The Wired shows enough similarities with organic neurological systems to be capable of sentience, and since it interfaces constantly with humans (by which it is defined, the product of the manifest is human. Mostly. She is literally God From the Machine (Deus Ex Machina).

Due to the merging of the Wired and the Real World, she has become a physical god in the combination of both realities. Hence she becomes almost a guardian, watching to prevent leakage between the two, reinforcing barriers that she herself installed. Or maybe she is just reinforcing the idea that the worlds are separate until humans can actually deal with something that pretty much amounts to a collective consciousness. In any case, because the Reset is her creation, she becomes a creator god in her own right.

Eiri Tries To Cause The Singularity
The Level 7 Protocol (which sounds almost like a thinly-veiled analogue of the TCP/IP stack, hypothesizing what TCP/IP v7 might be) blurred the borders between The Wired and real life. Lain was created to simultaneously carry the protocol in her head and also to act as a messiah to the merging of reality and The Wired. This is literally shown with the kids holding their arms up in the street to accept the "rapture" of Cloud God Lain In The Sky. While Lain is a created entity, living humans could transcend into The Wired and reach a singularity if they were to accept it (Eiri's plan all along). It all went badly when Lain rejected godhood and pushed the big reset button because she just wanted to live as a normal girl.

Lain is Haruhi is Shinji
After erasing herself from existence, Lain became Haruhi by locking away conscious memory of her powers and reinventing her personality. Haruhi, in turn, despairing at how ordinary the world seemed to her, imagined herself as a warped savior of humanity — that is, Shinji — and subconsciously made it into reality. However, Lain herself was an image of Shinji as he saw himself during Instrumentality. This causal paradox is fundamental to the existence of the universe; all of reality is an extension of Lain/Haruhi/Shinji. The Time Lords are people who understand how this works.

Lain is connected to the plots of both Steins;Gate and Haruhi Suzumiya

It hit me when I remembered how Okabe got his Reading Steiner: when he was a child, he became ill to the point of death, and the side-affects he was feeling then are the same ones he felt whenever a timeline changes. Now think back to how Nagato was at the beginning of Novel 10: really, really sick, due to Kuyou's viral attack against her. Now Lain is the closest equivalent to a data-entity in her own world; now, what if being in the Wired connected you to different timelines and different universes? If that were the case, then it hit me: Okabe received his Reading Steiner form Lain! Going further, I deduced that how Okabe received Reading Steiner was the same way Haruhi and Sasaki got their powers. As to why Lain did this, I cannot figure out, though...

Lain and Eiri start speaking each other's lines because they're just that meta

When Lan and Eiri finally meet face-to-face and suddenly seem to swap bodies, it's very confusing. The explanation for this is simply that, as hyperintelligent superbeings, they were both incredibly Genre Savvy. Lain had spent most of the series up to that point puzzling out Eiri's existence, while Eiri had been watching Lain from the shadows. Now that they've finally met, there's really only one way the conversation could go; recognizing that, they forgo saying what they're going to say in favor of saying what they know the other one is going to say.

Lain is the Wired
This Troper just finished watching the series, and immediately went to the WMG to get a second opinion on what just happened. Then he wrote half of this edit, and accidentally deleted it. We are flying by the seat of out pants here!

So the series reveals to us (as much as SEL "reveals" anything concrete) that Lain of the Wired was originally a "program" designed to, as Eiri said, "remove the barrier between the Wired and Real Life". Human Lain begins the series with no prior knowledge of computers, which implies that Human Lain is not entirely Lain of the Wired at the beginning of the show. The show also reveals that Human Lain is not living with her real family, and we never know if Human Lain even has a biological parent. Assuming this is all true, the series never really hints at a creator for Lain. If Lain of the Wired is a "program", she would logically need a "programmer" of some sort.

The KIDS experiment, created and conducted by our old and forgotten friend the Professor, intended to aggregate the psyonic power of the human subconscious at its strongest, and use it to do something metaphysical. It was performed about 15 years ago, roughly the same age as Human Lain. It was an experiment, and I don't know what it intended to test, but it failed either way. The merged psyonic subconscious of all of the children reacted poorly to being controlled (or manipulated) by the KID System, and in turn created such a metaphysical mess that it phased bodies through walls, drove men insane, and killed every single child networked into the machine. The Professor subsequently destroyed the machine so "it would never happen again". What happened? Well, with the KID System unable to control the psyonic power, the coalesced subconsciousness of all of the children left such a mental imprint on the universe (as it briefly ripped apart time and space) that it created a psycho-neural entity with no true body to reflect itself upon. Without a host, this psychic network would die as soon as metaphysics returned to normal (since its "birth network" of children and wires was broken), so it merged itself with the largest network it could find: the Internet.

Fast forward 15 years. The internet has evolved and grown in power and complexity, now on its sixth technical incarnation: Level 6 Protocol; known now as the Wired. The Wired is magnitudes more complex than the Internet of 15 years prior, and each individual device in the network is also incredibly powerful. It has moved beyond the constraining 2D page-like interface, and evolved into an immersive experience. There is so much power and inter-connectivity, in fact, that with the help of semi-legal nanotechnology developed from the technology used in the KIDS experiment, one could turn the Wired into their reality, connecting their neurology directly to the Wired and networking themselves. In the mean time, this slow evolution of complexity and new influx of psyonic energies from users has grown the electro-neural being from a slumbering consciousness on life support to a psyonic omnipresence with beyond-human, godlike power and total control of the host network system, i.e. the Wired. Thus Lain of the Wired was born, omnipresent and omnipotent within the Wired.

At some point, someone, or more aptly a group of someones, connected the dots. They figured they could tap into the psyonic power now latent within the Wired and use the collectively aggregated human subconscious to their own ends. They already knew about and were presumably using the nanotechnological chips to interface with the Wired, and were thusly had to be very knowledgeable about computers. They got together in secret over the Wired and formed a secret society to achieve their ends via pooling resources, and called themselves the Knights.

This one mad (and angry) coder named Eiri has a totally different idea. He knew about the KIDS experiment too, plus the electromagnetic wave currents in the earth's ionosphere, and thought that he could use the advent of Level 7 Protocol and his position within the tech industry to achieve godhood. He rigged up the new hardware and software so that the entire Wired would have his consciousness all over it, which would mean he could posses the "untapped" power of the Wired (then in use by Lain of the Wired), and so that it would tune into the ionosphere and use it to drag everyone's brain into the network while simultaneously turning the Wired into a network needing no "traditional" hardware, therefor gaining the most psyonic power possible, fusing Real Life and the Wired into one, and using it to permanently instate himself into the fabric of the universe as an immortal god of all men. The Knights saw this during the Level 7 Protocol turnover, and figured this was their god, and they were all going to pull a collective transhumanity (think 3rd Impact but with more individual will).

Lain of the Wired took notice of the intrusion and decided it needed a backup plan to continue living. It used the collective psyonic power of the Wired to create Human Lain, who was the childlike essence of the being that was Lain of the Wired, who had evolved beyond its pure essence. This basically wrecked Lain of the Wired, causing her to go dormant, but in turn created a girl with the age of the consciousness who could act as a physical avatar due to having uniquely powerful neurology and the mind of Lain of the Wired. Lain of the Wired gambled that Human Lain would be attracted to the Wired due to her origins and mind, and would be brought back into contact with what remained of Lain of the Wired, making Human Lain and Lain of the Wired each whole again and ultimately giving Lain of the Wired a human avatar to use for uniting the Wired and the ionosphere (an idea stolen from Eiri who was then already playing his part in Lain's plan) and permitting Lain of the Wired to evolve beyond the Wired.

The secret government organization (springing from the Roswell Incident as explained in the show) watched all of this go down and panicked, but never had the whole story. They sent out agents, snatched up Human Lain, went after the Knights, but totally missed Eiri. They put Lain in a false home from the beginning and sent her to school, which Human Lain fit into well because the childlike subconsciousness (of the children from the KIDS experiment and thus also Lain of the Wired) is Human Lain. Either she made herself false memories or the government brainwashed her; either way she came out not knowing who she was.

She spent a few years growing up with the false family of government agents, and becoming as human as she could. Meanwhile Lain of the Wired slowly continued to evolve as more of the nanotechnological interfaces were being used and the rest of the plans were put into motion. Human Lain became sympathetic, shy, and generally the Lain who we began the series with. Lain of the Wired became Bold Lain as it became more powerful, but lacked the strength to manipulate anything beyond the Wired and also the childlike essence it gave up to make Human Lain. When Lain finally did get on the Wired, Lain of the Wired finally knew it was time and used its influence to push the nanotechnological chip into Human Lain's possession at Cyberia.

Everything else in the series follows from that.

After that, Lain of the Wired and Human Lain fused more and more, causing all of the personality changes you see in Human Lain, and occasionally permitting Human Lain to use psyonic powers. When does Lain use psyonics? Human Lain created the manifestations of Bold Lain (which acted as both an avatar of Lain of the Wired as Human Lain saw her and Lain of the Wired itself) and Evil Lain (who was Human Lain's subconscious fears of who she would become).

Eventually, at the end of the series, Lain gets total control of all of humanity, the Wired is now in everyone's brains and the whole ionosphere, and everything is buggered. Human Lain and Lain of the Wired are now one entity again, but Human Lain was the more powerful personality, so she won out over the original Lain of the Wired. Human Lain has too much compassion for humanity, and fears her own power, so she chooses to hit the reset button on the universe, and removes herself from the picture by never having the KIDS project occur. Unable to kill herself, she exists now as a separate entity, a true god like Eiri wanted to be, but a god in an intentionally clockwork universe where she never existed.

Lain was spontaneously generated by the inclusion of Schumann resonance in Protocol Seven
Neither the Men In Black, Tachibana, nor Lain's supposed creator Eiri seem to know much about her... because they didn't create her. They just unknowingly made her possible by tuning the wired to the Schumann resonance. Lain isn't in the wired, or of the wired, she literally IS the wired... Lain happened when Gaia was inadvertently provided with a nervous system.

Lain is real. She used her powers to influence Ryutaro Nakamura to create Serial Experiments Lain as a way of communication.
Because someone had to post this.

SEL takes place on a virtual run environment, on a computer.

At the very least, it can be explained very, very well if you think about it this way. I really didn't get SEL until I thought of this metaphor, and I figured it could count as a WMG as well.

To make sense of this, let’s imagine the “real” world of Lain as a simulated computer run environment, like a massive, sims style world populated by “programs” (applications, if you prefer), or humans, who learn via artificial intelligence functionally identical to a normal human brain. These programs hold code, or brains, and their body itself is the program that can access that code (a "program shell", so to speak). Inside said environment, everything is connected on a “higher” and unconscious level, like the many programs being run on the same server, and connected via that as their code is held entirely upon that. These programs can communicate via an information transmission program called The Wired (which, just to clarify, exists within the virtual environment, not outside it), which does not do anything besides communicate information the programs have collected and wish to share. That is, until a program called Eiri creates Protocol 7 and adds it to The Wired, integrating the Schumann Resonance into it so that the “programs” can now connect unconsciously to the “server”, via running anything connected to The Wired (which is connected directly to the server/collective unconscious, or CU). For this metaphor, let’s say each person/program runs a Wired connected device three or four times a day on average, simply by idling and without any outside interference. Now that The Wired is connecting the programs and server each time they use it, the server and programs are slowly becoming one, giving programs theoretical access to other ones. However, they have no way to “run” this particular aspect of themselves, and are not aware of it to begin with, so until Protocol 7 does its job fully and the programs merge with and gain the server’s “knowledge” (that of the other programs especially, as they and all their memories are stored on it), everything should stay mainly the same. However, at this point, from unknown means, a program called Lain appears. She starts out as a blank slate with no information about The Wired, until other programs introduce it to her.

Unlike the other programs, Lain DOES have a way to access the server, because she can delve “inside” The Wired (which is, as previously stated, connected to the server). She can therefore rewrite program memories (as it’s stored in their code, which is stored in the server), communicate through the server/CU to any device with access to The Wired, and even “wipe” everything, computer environment included, and remake it with different parameters, repopulating it with altered variants of selected/all programs if she so wishes (as is done in the final episode, meaning the collective unconscious/server “holds” the world, and its existence allows for everything else’s). She does not know how to do any of these things at first, but learns over time.

It is important to note that this server is actually (at least partially) made up of the collective unconscious (all that code/internal workings the programs don't ever "see") of all programs in that environment. This means it has access to all their memories and code, but also means it is semi intelligent due to being made of the thoughts of the programs within that environment, and can act and react accordingly. The most apparent mark of this is that when enough of the programs in the environment believe in something, it actually creates that thing within the environment. This can be likened to many programs referring to a nonexistant program string, and the server/CU then having to create that program so as to avoid inconcsistencies and/or a crash. Alternatively, perhaps the operator of the server, if there even is one, created that program for exactly the same reason, or any unfathomable number of others (since to us, such a being would be an even higher, or perhaps "true" God). Thus, it is entirely possible, given the way this particular server works, that Lain started as nothing more than a concept, an idea- in fact, it is almost certain (especially taking the "alien", another product of our collective unconscious, and Lain being dressed as it later as support). The belief in that concept by other programs directly affected the CU/server, causing Lain to simply start existing solely through enough collective thought. Lain's existence story is speculatory in general, especially in the context of this metaphor, but it seems to make sense given what is shown. Whether Lain was apotheosized upon "birth", or if her concept only became deified over time in the collective unconscious, is unknown, and doesn't really matter given that by the time she interacts with anything, Lain is basically a God who doesn't know it- or rather, someone with access to the "code of reality", so to speak.

The reason for the existence of Lain's copies is unclear. They could exist due to any number of reasons- the varying interpretations people have of Lain forcing them to exist, her particular program being able to do multiple things at once, and thus the AI learns differently for each part of its operations which causes a "split personality", it's a manifestation of her abilities, etc. At the very least, in the environment's club "Cyberia", another program called Taro has been manipulating the code of visiting program memories to make them think Lain (one with a very boisterous and "wild" personality) has been there. In the code of their memory, that is now how she is. Their program code, ultimately stored on the CU/server, thus states a different Lain exists, and because of the above mentioned impact of the program's thoughts on the server, they are slowly bringing that version of her into existence (if she isn't part of the copies already). The most prominent copy of Lain seems to be one that is malevolent towards the "original" Lain, intentionally screwing up her relationship with the program Arisu and tormenting the "original" for seemingly no reason.

The Lain program gains access to a psyche chip early on, which allows her full access to The Wired from her NAVI by making use analogous to simply thinking. This means she needs only be "in range" of her NAVI to use it, no keyboard or mouse required, and using The Wired becomes extremely easy for her as she is not limited by what she can communicate to it. Of course, though Lain does not know it, she could connect to The Wired at any time, from any place, NAVI or not, if she so desired. She learns this later on, and from then on is able to alter reality to her liking due to The Wired's direct connection to the server/CU/thing that holds the code of the environment and everything it it on it. However, a problem arises...

Earlier, the program Eiri uploaded its entire “code” into Protocol Seven before its original incarnation was “deleted”/died. He now is integrated into the entirety of The Wired and has access to the CU/server, but has no actual dedicated “body” (or program shell), and thus no way to run his program in the environment. The "shortcut" is gone, so to speak, even if the program code itself is still there. Therefore, he can only affect things in or connected to The Wired, and nothing in the actual "real world" environment sans devices with direct access, which is why he can’t just force the other programs/people to merge with the server the second he is there. Once he dies, his program code is sitting in The Wired, running just as before, but with no way to interact with anything outside of it. He is thus less "powerful" than Lain, who can alter code from either the environment or The Wired, and could exercise complete control over it if she wanted. This is likely due to both Eiri and Lain's power being entirely dependent upon how much the other programs believe they can do (again, because of the CU). Eiri enlists the Knights for this purpose (and make them believe he is a God), while rumors of Lain's abilities get spread through The Wired without her doing anything- clearly, just the Knights believing in Eiri pales in comparison to the support Lain gets. While it is unclear if Lain existed only because of this, or if her powers came after her initial creation, is, as previously stated, unclear. However, Eiri most definitely existed prior to becoming part of The Wired. His initial connection with Lain is unclear- he either learned of Lain’s existence after she entered the environment, somehow created her inside The Wired and sent her to the simulation, or created a physical body for her when he noticed her code existed omnipresent in The Wired, and somehow put her or part of her code in that. It is unlikely he actually created a new blank program shell/body for her, as he could not do so for himself (at least, going by his later attempt, which doesn't go so well, though that may be due to the deaths of the Knights).

Because the program Lain is constantly connected to The Wired, which is connected to the server, and is done without the use of a device, Eiri can appear before her and attempt to influence what she does. This allows him to attempt his plan, which is to trick Lain into thinking he is truly God (how much he truly believes this is in question; he seems pretty deluded), and utilize her abilities to break down the barrier between the environment and The Wired, making his abilities unlimited and thus making him a "true" God. Also, as The Wired is connected to the CU/server, this will merge the three pieces (the programs/humans, The Wired, and the server/collective unconscious) together, joining everyone’s program code in the server while leaving the now blank program shells behind in the environment. Basically, he wants them to ascend to a higher plane of existence by becoming part of the server/collective unconscious.

After much discussion and argument/psychological torture tricks back and forth, Lain questions Eiri's existence as the God he claims to be, since The Wired hasn't existed since the beginning of time (or, in this case, since the environment was set up to run). She tells him he's just a stand in for the REAL God (which would be whoever started the environment or is keeping the computer the environment/world is running on maintained), which he cannot stand the idea of. He flips out and tries to manifest a body in the environment again, but is unable too do so correctly (more proof that he did not create Lain's body), instead creating a program shell that is visibly corrupted (as in, hemmorhaging tentacles, eyes, and mouths). However, his program code has been transferred out of The Wired and into the body- he is no longer even a "false God". His code is deleted by Lain smashing the body to death with the components of her room- with his brain/consciousness/code stuck in the malformed shell, he is gone, for good (until later, see below).

During the course of these events, Lain has been interacting with a normal program named Arisu/Alice/whatever as her friend. Arisu is a completely typical program- and has learned of Lain's abilities by the second to last episode. Already upset and concerned when she went to Lain's house to talk to her, the confrontation with Eiri causes her to break down, making Lain "realize" that the world/environment would be better off without her. Thus, in the final episode, Lain uses the server/collective unconscious to wipe the environment/world it holds, and remakes it mainly the same as it was before she came in to the environment, but with Protocol 7 removed from The Wired (so that the collective unconscious/server is no longer connected to the environment via devices) and with any memory of her written out of the other program’s code, adjusting for anything that involved her. Any deleted/dead programs are recreated with their memories from before preprogrammed in, hence Eiri, Chisa, and everyone else who was dead's continued existence. Lain herself now exists in a sort of limbo- since she's no longer in the environment, but her program shell/body cannot exist anywhere else, she's trapped in a part of the environment that technically does not exist- it's as if her program code was stuck outside the parameters of the environment's (literal, in this case) code, and formed there. She's "outside the brackets", I guess you could say- in javascript, something like "Environment World { blahblahblah, programs and their code go here, blahblahblah } Lain". She is trapped, and begins to be told off by one of her copies (who are presumably all with her, as they are part of her code/mind), but Lain sends that part of herself away. At that point, her "Dad" looks down, and transports her to what looks like the area of The Wired that she talked to the older man about his ESP experiments (read: low level server/CU alteration). After this, Lain is back in the environment, though she may reside mainly in The Wired- and how did she get back in? Presumably because her "Dad", ie. The "real" God and owner/maintainer/creator/whatever of the server stuck her code back into the environment where it belonged.

Serial Experiments: Lain and Death Note share continuity; Light and Lain are contemporaries.

Ryuk's grin is a visual shoutout to Eiri's grin. Similarly, many shots of L throughout Death Note are visual shoutouts to the creepy way of portraying peoples' faces in Lain. Lain is visible in one shot on the Yamanote Line with a friend when Light gets Raye to kill all his coworkers in Death Note.

Lain encounters GLaDOS

In fact GLaDOS had a part in both Lain's creation... For Science!...

  • More accurately, Its all Aperture Science's fault. They're uniquely known for their capabilities of getting into zany schemes like The Wired and the crestion of Lain.
Lain is actually a Magical Girl

Fortunately for Lain, she was able to control her witch form and remain herself and a sort of Noospheric god.

Lain was created by the government and the lines between reality and the Wired were already blurring
Masami Eiri and Tachibana laboratories knew this was happening and tried to create someone who was able to move between the worlds and keep balance. The government took control of the project before they were finished with it and created Lain. Lain's adoptive parents were hired by the government to keep an eye on her and make sure she doesn't go haywire. They may even work for the government themselves.

Not knowing what happened to the project, Eiri kills himself to enter the Wired and keep it from taking control of the real world. Eiri and the rest of Tachibana laboratories eventually find out about Lain through the Wired, but don't know if she's the project that they developed or not. Hence, why they don't know anything about her, but Eiri still claims he created her. The other Lains in the Wired are other people's attempts at duplicating the project (The Knights for example), or Lain prototypes that got discovered by The Knights. (Kind of like the KIDS project.)

The Wired and the Warp are the same, or at least different aspects of human subconciousness
The Wired, as stated, has the properties of the Jungian 'collective unconcious', while the Warp is basically human emotions manifest itself into reality.

Yasuo Iwakura is the real God and Lain is the Messiah.
In the last episode, Lain of the Wired states that the Wired merely recieves its powers from being connected to a greater entity. Since Lain originated as scattered pieces in the Wired, she herself can't be God since she is part of a subordinate entity. Lain figures out with Eiri that his plans were inspired by God and it doesn't make sense for unconscious, egoless pieces to convince someone to assemble them, so someone else must be God and made Eiri assemble Lain.

Now, who is God? Yasuo Iwakura. After Lain erases all humans' memories of her, he's was only one who remembers her and he hosts (he says he's the one providing the food) a tea party for her in the sky. He is the greater entity the Wired is connected to. He was faking his identity and pretending to be mortal before Lain reset time and he still is towards everyone except her.

Lain actually is his biological daughter and the Messiah. Lain has many parallels with Jesus; she was incarnated through a human but had preexisted her incarnation, her presence on Earth is a cataclysm for change in the laws of life and she leaves the Earth only to return to her friend for a short while.

Lain IS Protocol 7.
Eiri uses Protocol 7 to unite humanity's collective conscious in the Wired. Lain is an AI created to lead humanity to this end, or maybe she was Protocol 7 all along. Her mere existence allowing for the Knights ability to hack reality, the Wired leaking into reality etc. All due to Artificial Intelligence No 7 - AIN 7 - LAIN