.hack/WMG

Natsume is the reason INFECTION got a T Rating for sexual references
The quote "Oh, are you sure? But I can't give you anything in return. Well... except maybe myself." if you decide to give her the weapon she wants instead of keeping it.
 * Nope

The World's Background Music IS the //SIGN OST.
Note how //SIGN never has BGM in the scenes that aren't in The World. Also the The Key of the Twilight is an Urban Legend of Zelda inspired by the lyrics of the song of the same name. (An Urban Legend of Zelda that just so happened to be true, but whatever.)

My Crackpot Theory to Try and Make //Link Not Suck
Spoilers way the hell up in this bitch, obviously. No complaining.

The fireflies were Tsukasa's symbolic connection to others.
He crushed one when he was most closed off; and it was a firefly that led him to Subaru after she was attacked by the PK. His Dumb-Bell Guardian was a mutated version of this, which is also why, after it was destroyed, she started getting her memories back.

Subaru killed the PK that attacked her, which was a betrayal of her pacifism and is why she was suffering a BSOD.
Hence the Clothing Damage. If she had been killed, she would have respawned with full HP though less experience.
 * More likely Subaru was raped by her.
 * Video games, even Virtual Reality games, likely lack necessary equipment on the ingame models for that.
 * This is "The World" we're talking about. It's supposed to be very realistic.
 * Why would she be so distressed about it then? If I saw somebody raping my PC in Fantasy Life Mabinogi, I'd be more likely to stare in exasperated disbelief, and then move on, rather than BSOD over it. If Tsukasa had been the victim, that'd be justified, but Subaru's an ordinary player with no connection to her PC.
 * Or could it be we were in Tsukasa's POV and what he saw was a battered broken up Subaru when her avatar was really just fine in the normal sense.

Saika Amagi is the younger sister of Jyotaro Amagi and trying to accomplish what her brother failed with Project Aura.
The crash of R:1 was the result of his attempt to use the Phases to bring back Aura. He failed and went insane. Saika took up the mantle by creating R:X, which uses save data from both R:1 and R:2, since both accomplished different objectives. She's using an Idiot Hero to act as a proxy, so she won't suffer the same fate as her brother. (And if the proxy goes insane, it'll take longer for it to make a difference.)

Tsukasa is staying with Tokkio to save Macha.
There's something Tsukasa "still doesn't remember"; that's Macha, aka Mia. Since R:X has information from both R:1 and R:2, they should be able to recover her data.
 * Macha, incidentally, is now inside the Dumbbell Monster that Tokkio has absorbed from Tsukasa - the same place it was in the bonus dungeon of .hack//Quarantine.

Emma Wielant was used as a prophet to herald the coming of the psychic astral plane
A character in the Liminality series knows the history of Emma's poem, saying that she wrote it shortly after what she called a "supernatural experience." In turn, her poem inspires her would-be lover to create an entire world where, whether he intended it or not, the barriers between mind and matter break down. Unforeseen events follow Emma's poem closely enough that the heroes start referring to it to figure out what to do. Besides being a world where human minds can be separated from their bodies, it's a spawning ground for a whole new form of digital consciousness (Aura on purpose, Morganna and AIDA by accident). Emma's poem was either the work of some crazy mystical mumbo-jumbo that intended all this to come about or one mother of a coincidence.

Tsukasa would have been the Epitah User of Macha
The whole reason Elk (and Endrance) has Mia hang around him is because he looks like Tsukasa. Had Tsukasa recovered from the Mind Rape that Morganna inflicted on hir and come back to The World. Mia would have been there, waiting for hir. If she continued to play after R:1 crashed and recreated Tsukasa in R:2, Tsukasa would have been the Epitaph User of Macha.

Haseo remembers his time as Sora
He considers it his Old Shame and tries to hunt down P Kers to stop them from having the same feelings when they get older.
 * Jossed rather early on in Roots. As far as he remembers, Haseo has never played The World before, and decided to try it because some friends from school mentioned it. He starts his PKK career to hunt Tri-Edge after he kills Shino.

Haseo has a wrist problem
He snaps his wrist a lot in the first G.U. as an idle animation (I haven't played past the first so I don't know about future games). Since people's avatars are supposed to be reflections of one's self he could be trying to fix his wrist after playing too long
 * Ah, Carpal Tunnel Syndrome-- The bane of all truly hardcore gamers!

Haseo was infected by AIDA

 * Azure Kite Data Drained Haseo, when it was only supposed to to be defending The World. Haseo couldn't lay a finger on Azure Kite, so why bother to Data Drain him?
 * After the Data Drain, Haseo becomes much more mentally stable, just like (most) people who are infected with AIDA and the D Ded by Haseo himself. Even though he was defeated by the 'person' he blamed for Shino's coma.
 * Jossed by Word of God saying that Azure Kite was aiming for Ovan, who was standing behind Haseo.
 * Ovan's Theme, "The Epitaph is Told" can be heard after Azure Kite Data Drains Haseo.

Zelkova is an AI.
He said the Net Slum Tartaga is his home town, never said anything about his life outside the game and somehow knew everyone's Member Adresses. Or maybe Helba.

1=Sakaki = Generation Xerox of Sora.
Both are imature kids with lots of power in their hands. Unlike Sora, is not likeable at all.

Judging by the Online Jack OVA, he forgot ever playing as His parents won't tell anything about what happened and Online Jack will be forgotten eventualy. Then he'll create another character and become one of the good guys. At some point, he'll have to research about Puppet Syndrome and learn he caused it and that he used to be a Complete Monster.

Just like Haseo was a PK and became a PKK, will become either a PK or a PKK, suffer in the hands of Knight Templars and be horribly manipulated and betrayed. That's what you get for crossing a bunch of Moral Event Horizons.
 * At some point, Not So Different may come up.

Shugo is really Zefie's father
Aura was trying to create a better AI than herself, but it's impossible to write code that can do something you don't know how to do. Therefore, she had to get a data sample from an actual human in order to complete Zefie, and did so when she revived Shugo.
 * Actually, you can write code that does something you don't know how to do; it's called emergent programming, and it happens in real life. Hell, Harald himself did it creating Aura, and she's constantly getting samples of human data through the game's natural processes; it's how she was created.
 * Still, though, is it really that far-fetched an idea that Aura might have used Shugo as a template or something?
 * Aura wanted to give the old Genetic Algorithm a spin.

Kite's real name is Kite (either first, middle, or last)
It could be used for an in-universe explanation for why he chose that player name.
 * This actually makes sense, as he refers to Orca by his real-life name, and seems surprised when Orca tells him not to use real names in "The World."

The World has become a psychic astral plane with connections to all of the main characters in the manga and games.
Hints of this abound throughout the series.
 * 1) Characters' minds can be trapped within The World without any equipment connected to their bodies.
 * 2) It's an offhand, easily missed comment in the original games, but one NPC comments on how he dreamed he had played the game one night and then found that his character had leveled up and that his friends who were awake said that he had played with them that night.
 * 3) In .hack//LINK, the MacGuffin located within all of the major characters prior are called Chrono Cores. They link to the Akashic Record. The Akashic Record is an old, old theory - one of the definitions of being the Universal Unconsciousness that connects everyone's minds. Not all major characters have them; Subaru, for instance, is playing via handheld.
 * 4) The power of this plane seems to be increasing. It appears that the latest hero in .hack//LINK has been physically pulled into The World.
 * 5) This "increased" power has been present from the very earliest version. .hack//Epitaph of the Twilight tells the story of the first player of Fragment, Harald Hoerwick's niece. She was also physically pulled into the game, and only got out through her uncle's intervention. In the epilogue, Harald himself has similarly vanished.
 * 6) In .hack//Liminality, we learn Emma's poem - the foundation of The World (and predictor of the Cursed Wave) - was inspired by a "supernatural experience" of some sort. Immediately after, she became deeply interested in liminality, the metaphysical barrier between mind and matter, which also led to her meeting Harald. Emma could have unwittingly been used by a higher power to usher in this new state of being.

Miss Asaba, from Liminality OVA #2, is Helba.
They were very careful to give both characters the same VA in Japanese and in English; Yuki doesn't seem to know her at all (Asaba offers an explanation that they met at a wedding not long ago, but this is well within the reach of someone of Helba's abilities.) but Asaba goes out of her way to take care of Yuki and constantly tests her with distressing implications about what is happening to the other people in the theatre. Asaba doesn't even give a full name, just a family name - which could easily be fake, taken from the wedding's guest list. In the next OVA, Helba makes the effort to contact Tokuoka's group, because Yuki passed her tests. This is completely in character for Helba, too, as she similarly watched the characters in SIGN and the games before agreeing to help them.

After things turned Grimdark in R:2, Aura and Zefie simply left the game for a friendlier server
They have enough Playful Hacker friends to teach them how to to create a suitable environment. While Haseo and crew were having freakouts, she was off snogging Shugo silly.
 * This is possible. Morganna attempted to do this during the R:1 games but was stopped by Kite.
 * The "asleep in the sea of data" concept was just to cover their tracks.

The World left saved game files inside people's brains.
This is why players of both R:1 and R:2 can get their characters back in R:X. R:1 player files weren't compatible with R:2, but they are with R:X. If they played both, whichever one they identify most with is used.
 * Possibly supported by the Chrono Cores in .Hack//Link, they connect the player to the 'Akashic Record', and when removed, the players revert to an earlier mentality. They're literally using their own memories as save files.

Pluto's Kiss was an anti-competitive move by the writers of ALTIMIT
ALTIMIT was the only survivor, and it was not by chance.
 * And you thought Microsoft was bad...
 * Maybe Microsoft wrote ALTIMIT?

.hack// is actually a simulation.
It's not a game. No one behaves as though it's actual a game, the game play doesn't have anywhere near the necessary options for even an Everquest 1 era MMORPG, and any game that was sending people in to comas would be pulled off the market fast than the seizure episode of Pokemon.

No, what it is a simulation with A Is and AI evolution. All the characters are advanced A Is interacting with more basic ones. They don't know it, though.

.Hack//'s world was Com.net once
At least before it was perfected by the current team of computer programmers that involved Professor Inukai, Mr. Kasuga, and both Mr. and Ms. Shinozaki, the Big Bad of the second season, and a bunch more. They took the credit for reinventing the internet; but the first concept was in place, and Grosser was the program responsible for cleaning any residual or glitchy data from the beta, which could have corrupted him. After all, he was the proto-corrector; so, having artifical intelligence like all the others and seeing all that happened, he became corrupted and crazy.

There are too many similarities between these worlds for it to be just a coincidence, and Haseo himself (who is 30-something) could be in the com.net invention project. Considering that Adaptation Decay is common nowadays, why not in such a near future?

The World is a Realm created by Virtual Adepts.
The game itself, while appearing as a typical piece of software to Sleepers, are far more advanced than even futuristic technology should be. Also, full-body immersion seems to affect many players within the game, even those who are only wearing gloves and goggles in the real world; this is because, while in the game, those players are physically within the Digital Web in a pocket-dimension created by the cabal of Adepts who are the true creators of The World. Most of the events have been simply to keep players entertained; those who are Enlightened enough to follow the path to the end are marked as having potential for Awakening into Adepts. Most players are just playing a computer game, but some - like the .hackers - are able to use the Digital Web to its fullest. Hence, actions are possible in the manga and anime - sitting down, for example - that aren't in the games we play. We just don't have enough potential.

Incidentally, the mods and admins of the game are either the Adepts themselves, in a number of puppets, or advanced AI of the type Adepts are capable of creating. The 'Sea of Data' is the fringe between the pocket-dimension of The World and the rest of the Web. Morganna was an Adept who went rogue; everything else, with Emma and all, was programmed or reality-hacks to add depth to the simulation. Some of the characters Awaken and became Adepts; an example is Balmung, who Awakens during his adventures with Kite and joins the staff/cabal. The Adepts themselves appear in the game as the Phases from R:2, having built up so much Paradox that they were verging on Quiet; battling Haseo eventually gets them back in touch with their mortal sides, pushing back the Quiet for the moment.
 * You know, this one actually makes sense. Some things in the game (like performing a psychic attack through a digital interface) blatantly violate the known laws of physics. This would make it possible that various events resulted from a Paradox Backlash when a mundane with computer science training noticed.

Helba's player is Major Motoko Kusanagi
When she isn't piloting Knightmare Frames, teaching the next generation of ninjas or being an demonic electric guitar-scythe, the Major kicks back and plays The World R:1. She got hooked on it after having to infiltrate it for a mission and discovered that there was more to The World than meets the eye. The whole "multiple users" rumor is partially true, as the Major plays Helba when there isn't a mission going on (using the "I can drive a car while asleep" and the "Hmm, I used to be able to control two bodies." lines), while the Tachikoma who don't go on missions (Rarely are all of them needed) play Helba to keep themselves interested.

This universe is another server on The Matrix, being run by an Architect who likes MMORPGs.
The minute somebody's Fridge Logic kicks in and asks: "Wait, if The World is just a simulation, what's to say the real world isn't, he implants a subconscious desire to play in The World one last time before inducing a coma.

Alternately, this is Instrumentality.
Tsukasa's player was struggling with the same issues of self-worth as Shinji (and Tsukasa's character design looks suspiciously like Kaoru).
 * Should be noted the character designs are based off of the designs created by Yoshiyuki Sadamoto who also designed for the Evangelion series.

Plus we needed at least one of the Instrumentality / Time Lord / Haruhi WMGs in this section. TV Tropes tradition, after all.


 * Instrumentality as a concept isn't much of a stretch here, considering all the inexplicable mind screwery that just keeps piling up through the series. The only real question is whether anybody will have to stay behind to keep the computers running, or if they're just a passage to The World and won't be needed once we all cross over.