Code Lyoko/WMG

XANA is Nyx
The monsters are Shadows, William is Takaya, Ulrich is Akihiko, Odd is Junpei, Yumi is either Yukari or Mitsuru, Jeremy is the MC, and Aelita is Aigis. The Lyoko forms are Personas (who seem to only know Physical skills) and the scanners are Evokers.

XANA is Franz Hopper.
Fan-theorising on Lyoko Freak has suggested that Franz Hopper created XANA's AI using his own brain-waves. The catch? Once Franz was dead, how does the supercalculator tell the difference?. Also, it's at least heavily implied by Franz's journal entries that by the end he was a couple of sandwiches short of a picnic; an insane human mind is likely the last thing you want to try to model as a computer program, even on the world's most Badass Quantum Computer. It's entirely possible that a combination of this insanity, simple data corruption and the inherent instability of a Multiple Agent System (like the Marabounta, which didn't even have an AI and still went badly wrong) caused Franz to either merge with XANA or replace him outright. Result: Instant lunatic, just add water. The result is either some strange form of Split Personality or a massive Xanatos Roulette that has yet to see frutition. Or both. There is some evidence for this:
 * First, XANA seems quite happy to allow the Lyoko Warriors to survive between attacks (in "Hot Shower", he actually destroys a meteor headed for Yumi when he could have let it kill her).
 * It's worth noting however that XANA's goal that episode was to destroy the Quantum Computer with Aelita in Lyoko to trap her inside it. The meteor would indeed have gone on to kill Yumi, but Aelita would be separated from Lyoko contrary to XANA's plan.
 * Second, XANA seems perfectly willing to help with threats that weren't created by him and therefore not part of his plan (like the Marabounta, which was one of Jeremie's programs that went wrong; with the Warriors unable to deal with it on their own, XANA sent in monsters to help them and prevent Lyoko's not-convenient-at-that-point destruction).
 * Third, in one episode XANA attacks just before Aelita has to undress for a medical exam, the possible act of a father trying to protect his daughter's modesty (or just the writers being bastards, since Sissi had been shown undressed (again) moments before).
 * Fourth, we never did learn exactly where Franz was being kept before Lyoko was temp-deleted (the tower in Sector 5 was suspected by fans, but nothing was ever proven).

XANA is Antea Hopper.
A variation on the above, for those who think Franz wasn't several sandwiches short of a picnic. In this case, Antea was kidnapped sometime during Franz's last days on Project Carthage. In disgust, he leaves the project and uses its resources secretly to rescue his wife. Trouble is, the MIB have turned her into an AI construct. Counter-theories to the above bullet points follow:
 * Letting the heroes survive between attacks? We've got two theories on that.
 * A: Antea-XANA has a GLaDOS-like Morality Core that malfunctions periodically to make her do various diabolical deeds.
 * B: Overclocked human brainwave-based AI means overclocked mood swings. Every attack is a Roaring Rampage of PMS.
 * Helping out in Enemy Mine scenarios? Simple self-preservation protocol, not too far off from the "XANA is Franz" theory above.
 * Attacking to get Aelita out of a physical? Maternal instinct.
 * Franz's whereabouts during the big cliffhangers? Simple: he operated out of Sector 5 until "Revelation/The Key," in which he depleted his power to restore part of Aelita's human memories. From there, he escapes to the Internet proper, bumming energy off Windows XP users to reconstitute himself. After the Ten-Minute Retirement of Lyoko at Season 3's end, he returns to the supercomputer to secretly affect repairs on the Skidbladnir, occasionally popping up to rescue Aelita from the Digital Sea if her wings don't kick in.

The story is the final chapter of the .hack saga, .hack/LYOKO
Sometime after the current .hack series, the World is pulled offline permanently. It turns out that Jun Bansyoya's journal lied, and Harold Hoerwick returns from years of study into molecular manipulation to gather up the remaining The World computers and reconfigures their data into a new version on a quantum computer, creating Lyoko. He then retools Aura into a more realistic version, Aelita, and prepares to finally bring her into the real world as a testament to his love for Emma. He even goes as far to create a fake identity, papers, and photos, so that he and the new Aura will look like a convincing family and be able to hide from CC Corp. Something goes horribly wrong, though, and Morganna remanifests from the hidden depths of the New World as XANA.
 * There is a fanfic in which XANA crosses over to the world of .hack//Sign and the players therein have to fetch the Lyoko cast to help defeat him.
 * Could I possibly have a link to this?

Code Lyoko takes place in the Marvel Universe.
C'mon, Marvel bankrolling the short-lived Code Lyoko toyline and MoonScoop producing a short-lived Fantastic Four animated series? It can't be a short-lived coincidence. Now that XANA's gone, our heroes will move to England, become the Ultimates X-Calibur team, and work in at least three Doctor Who references a year.
 * On a related note, Ulrich is a Skrull, as are both his parents.
 * Nah, only Ulrich's Jerkass father is a Skrull. However, Ulrich will use powers derived from his Skrull heritage to usurp the position of Captain Marvel.

The Supercomputer has enough power to determine The Ultimate Question of Life the Universe And Everything.
In a rare occurence of reaching through the other side of the Fourth Wall Mail Slot, it's "How long will CL fans have to wait, in years, before the entirety of Code Lyoko comes out on Region 1 DVD with French audio?"

The Men in Black are actually Clock Roaches.
For starters, notice that throughout the present day of the series, Franz Hopper has never taken corporeal form. Turns out his doing so would trigger a paradox and/or causal loop that would spell the end of the Multiverse as we know it. Thus, the Men In Black needed to ensure a Stable Time Loop by forcing him to shuffle off the mortal coil, through death or other means. Since death would throw a wrench into future events, they chose "other means" - if Franz and Aelita didn't evacuate to Lyoko of their own accord, they'd drag them into the scanners. Kidnapping Antea (and possibly turning her into XANA or a XANA-prototype as denoted above) was insurance to make sure Franz would continue his work on a virtual world derived from Project Carthage and eventually take up permanent (or at least permanently disembodied) residence in the end product.

Aelita learned how to use Energy Fields in the Time Skip between Seasons 2 and 3 by marathoning Naruto.
Alternatively, she knows Jump Super/Ultimate Stars.

Harold Hoerwick was on the Project Carthage staff.
Largely a concession to the ".hack//LYOKO" theory above. Other notable scientists include: Furthermore, the Project Carthage staff is the group responsible for the creation of many A.I.s.
 * At least two Doctor Browns
 * At least one The Doctor
 * Dr. Tadashi Hikari or Thomas Light, continuity depending
 * Dr. Albert Wily, continuity notwithstanding
 * Which means that XANA's specters are related to the Maverick Virus.
 * A young Academician Prokor Zakharov, who eventually modeled his goggles off Franz's specs and Suiseiseki's eyes

XANA's name is actually "Xana".
When Franz Hopper created the super computer he designed it to use a case-insensitive character encoding to get a (very) small boost in performance. Hence why everything, including XANA's name, appears in all caps.
 * Actually, no. The reason for the mostly-caps thing is that the "Lyoko Font", Gunship, has nearly all the lower-case letters appear in uppercase, with the exception of "b" and "d".

XANA is a prototype of the Hunter-Seeker Algorithm.
Formless in its structure, horrifyingly versatile in its offense, XANA's activities fit the Hunter-Seeker's FMV to the letter.
 * But if the fake Franz was right and XANA was made to combat multi-agent systems, how did Jeremy manage to overwhelm it with one?
 * XANA follows the Alien Crossfire rules: Jeremy wasn't OHKO'd because he had Algorithmic Enhancement, and mounted a successful counter-offensive because his Probe Score was +5.

Franz Hopper isn't Harold Hoerwick
Although Franz and Harold had the necessary knowledge to accomplish their goals separately (destroying Carthage and materializing Aura respectively) neither had the necessary resources so they decided to work together to accomplish their goals. However, Harold was kidnapped and tortured for information by the Men in Black, he eventually committed suicide, but not before revealing he was working with Franz. The Men in Black then kidnapped Antea hoping to use her as a hostage in order to force Franz to work for them. In order to ensure she wouldn't escape or kill herself they virtualized her using an older model scanner. However, she managed to escape onto the network and eventually made her way to the super computer where she became merged with Morganna and they become XANA. Furthermore, when Aelita was virtualized onto Lyoko, XANA merged her data with Aura's (creating Aelita Stones) in order to both protect her and prevent Aura's materialization.

XANA was made with Progenitor technology.
Yes, yet another SMAC-themed WMG, I know, but bear with me.
 * First, see the Hunter-Seeker WMG above.
 * Second, consider XANA's modus operandi: the manipulation of electric current, electronic computational functions, and bioelectric impulses to affect a variety of attacks. These come as easily to XANA as the manipulation of electronic and thermal resonances for Progenitors - in fact, the latter is their primary communication medium.
 * Finally, nobody seems to agree on which set of gender pronouns to refer to XANA with, if even to use ones denoting gender at all: the show has a secure grip on referring to XANA as male, while several Fanon interpretations depict XANA as female (if not having a separate female avatar to ship with William), the Let's Talk Tech team at Lyoko Freak seems to like gender-neutral pronouns, and the games (or at least "Fall of XANA") switch between the three with reckless abandon. Solution? Reference to XANA is designed with gender fluidity in mind: much like in communicating with a Progenitor, it doesn't matter which pronouns you use or how frequently they're shuffled, as long as it's clear you're referring to the same entity the entire time. Also, it's either this or we take the Squick route like with Pikachu and Vaarsuvius.

XANA turned William into an Espada.
Jeremy provided the BFS, all XANA had to do was write all the jokes at Ichigo's expense. And possibly Chad's, with all the times William wound up getting Worfed.
 * Meaning, of course, that all Jeremy had to do in the end was Reject XANA's programming.
 * Also, Antea Hopper survived...as a Mod Soul eventually installed into Mister Puck.
 * Not to mention Ulrich's dad is a Bount in addition to being a Skrull as denoted above.
 * Nah, Ulrich is a kinda similar name to Uryuu... I bet he's a Quincy.
 * Couldn't be. Ulrich lacks mad sewing skillz.
 * Ulrich is a Soul Reaper. He fights with a sword. Odd's the Quincy.
 * No, Yumi is the Soul Reaper. Take a second look at her first Lyoko outfit. The right side of the kimono is over the left.

Franz Hopper survived. AGAIN.
Admit it, the guy never seems to die when he makes a Heroic Sacrifice, and whenever he shows up afterwards, it's always a good thing he could heal. This means, of course, that he'll turn back up eventually, but it'll take something as drastic as Un Monde Sans Paix to necessitate it. Why does the dub deny any personal attachment to Paris? Simple: Lyoko or some analogue actually exists, and the MIB aren't all that keen on admitting the French beat Area 51 to it. The lack of editing on MoonScoop's part, by association, is a subversive measure to break the Masquerade, spearheaded by none other than Sharon Mann herself. And possibly himself.

Aelita could come into some massive alimony payments should she choose to forgo her Undead Tax Exemption.
Let's see, that's 10 years of data stasis and emotional damages thereof, plus child support from Franz (because he's STILL ALIVE, as noted above), multiplied by punitive damages to be assessed against the Men in Black, minus a rod of U-235... I think I'll just toss her this catalog of Upper West Side apartments and she and Jeremy can call me back when they find something good.
 * Minus unpaid tuition for Kadic, which seems to be a private school.
 * Nah, Jeremy hacked in a free ride scholarship for her. Because love makes you do those sorts of things.

Sissi is a clone.
Blame Carth for semantically introducing the possibility that Sissi might not have (or have had) a mother. Then again, tossing a cheerleading baton into the air, never to return, isn't something that can be easily done with natural human strength. (Technically, she did it twice, but I (you should know the one by now) am using "XANA Awakens: Part 2" as my frame of reference because XANA wasn't mucking with the Earth's gravity that day.)
 * Wow...I just wrote that cause it was missing, and someone's already commented on it. O_O Anyway, all I think is that Sissi's suspicious lack of mommeh is, well, suspicious. My guesses fall in several categories- one, she's a clone, like you said (which would make for a really cool plot if she ever joined the Gang), two, Jean-Pierre is at least not her father (maybe she was a foundling or something, abandoned on the Kadic doorstep...but that's straying into Fanfic territory), or three, I'm reading too far into it and Sissi's mum is simply not important.
 * Perhaps she's the mastermind behind all the conspiracy!
 * Perhaps Sissi's mom is Antea Hopper.
 * Hey, this works! Canon says Sissi's mother is alive and away. So is Antea.  The only hole in this theory is that Sissi must have been born during Franz's tenure at Kadic.

Taelia is Aelita's half-sister.
Antea Hopper is still alive. She escaped the custody of her kidnappers after some 5 years thanks to the help of one of The Men in Black who fell in love with her and betrayed his cause. Believing for a while that her husband and Aelita were dead, she started a new life on the run with her savior. A girl was born some 2 years later, and Antea gave her a Significant Anagram name of her lost daughter: Taelia. The father discovered some years later, from a lasting The Men in Black acquaintance, that Waldo Schaeffer survived but was almost captured again, and then disappeared for good. Antea still wanted to find him and Aelita, but doing thorough researches was difficult and risky. After many years, they uncovered his last whereabouts: he had lived under the name Franz Hopper and had been teaching at Kadic Academy. To not attract the attention of any potential The Men in Black surveillance, Taelia was enrolled for a short while so that she could glean some information about Franz Hopper by peering through the school files or discreetly interrogating the principal. She pretended being an orphan to deflect any question about her parents.

What? That makes a LOT more sense than the Identical Stranger scenario...
 * If she dies and Jeremy installs her DNA into Aelita, will it unlock her true power? Just curious.
 * Extra credit for getting your timeline right - 7 years is absolutely spot on, which took this troper about 6 minutes to confirm. Anyway, isn't there an OVA on the way explaining more about Project Carthage? You may be right...
 * Actually, that OVA got sacked. There's a novel series on the way, but as far as I can figure, that's an alternate continuity.
 * Supposedly, there are three CL movies planned, but they're stuck in development hell at the moment. As to the novels... we'll see.

Project Carthage (though not necessarily Lyoko or XANA) was originally a time-travel project.
Instead of Carthage being a tactical reference, it was their goal. They could already travel forward in time, by uploading themselves and then having the programming frozen from the outside, rematerializing once the physical computer reached the intended destination, having travelled at the speed of 1 second per second. They did not, however, have any idea what they were doing trying to go into the past. The 24 hour limit was either a result of Jeremie's inability to unlock it any further, things went haywire if they went too far back, they decided it wouldn't be worth going back in time too far since anyone who died in the interval would still be dead, or, this troper's favorite, nothing exists more than 24 hours before the present.

Code Lyoko takes place in the CLAMPverse
One of the rules of the CLAMPverse is that the dead can never be brought back to life, despite this time travel is possible.
 * Speaking of CLAMP, there's an intersection with Code Geass by proxy: Antea staged her "kidnapping" with a little help from Emperor Chuck for the sake of a round of Xanatos Calvinball that will eventually culminate with Grendizer and Mazinkaiser being placed in the same Super Robot Wars game...except 'Dizer uses its French name "Goldorak." And it ships with any Pizza Hut order with two large 1-toppings and breadsticks.

Code Lyoko and Oban Star-Racers take place in the same world
Not only do they share at least one creator (Thomas Romain), but a motif of facial tattoos is present in both series. Odd has several on his face in his CGI Lyoko Warrior form, and in hers, Aelita has two thick vertical lines on her cheeks, similar to the ones Molly and Maya have on Oban Star Racers. Coincidence? This troper thinks otherwise.
 * hmm...Maya, you say?
 * M-Maya? Oh God, it's Carnegie Hall all over again...
 * This troper thinks you're on to something. OSR takes place in either 2081 or 2082, judging from a banner glimpsed in a flashback to a time shortly before Maya Wei's death. Assuming that Jeremie was eleven or twelve in 2005, that he and Aelita grew up, married, and had kids, that pink hair is some sort of recessive trait, that Maya was somewhere in her thirties when she died in 2071/2072, and that Maya was actually French... Jeremie and Aelita could be Eva Wei's grandparents. (Unless this troper's math is wrong. She double-checked, honest!)

Jim is a Solid Snake, and Code Lyoko is an Alternate Universe of Metal Gear.
Jim has plently of Noodle Incidents, and they both have brown hair. I imagine that Jim is really Snake in a world where Liquid died in a horrible accident, Ocelot's plan never got past "Snake Eater", and Snake really did get to stay retired. Snake himself got fat after years of enjoying himself, but fled the country and moved to France when he realized he might be tracked by a-li-lo-a-li-le La-Li-Lu-Le-Lo. As for Lyoko, it could be, and the MIBs in Aelita's flashback being  who wanted to kidnap Aelita so they could blackmail Franz,.


 * William is Psycho Mantis, by the way. "You LIKE Oban Star-Racers, don't you?"
 * Taking things into Konami's expanded universe for a stretch, Franz Hopper is actually an alias for Waldo Schaeffer Petrovich Modnar. Which makes Aelita a Snatcher of Antea Hopper intended to keep up the Masquerade of a nuclear family. Except she accidentally became human through interaction with XANA, who happens to be an Immortal. A decade later, Jeremy and pals Shot The Core so that Aelita could spend her days in peace, playing children's card games.
 * Further addendums to the above:
 * The laser satellite is actually, which would make XANA.
 * Jeremy may or may not do all his less scrupulous hacking under the alias "Shalashaska," depending on whether he can remember to put in that last S (Lord knows I have trouble with it).
 * The Hoppers Schaeffers Hell, maybe both could be distant offshoots of the Gurlukovich line, following a bizarre and improbable path to rebuilding Russia that was mostly extrapolated from an old Betamax of the Soviet movie Aelita, Queen of Mars. Insert your own Zone of the Enders joke here.
 * The only reason Jeremy says the supercomputer can't bring people back to life is because The Sorrow would have his ass for it. See also Big Boss's spiritual shenanigans in The Last Days of Foxhound.
 * Yumi is actually a Model 3 Test Subject, complete with rack designed by Team Ninja.

Jeremie wasn't the first person to find the super calculator after Franz Hopper and Aelita were trapped on Lyoko.
The people who originally found it they also tried to materialize Aelita, but instead only succeeded in creating imperfect infant copies of her, which they adopted and named Jeremie and Taelia. At some later point one of XANA's attacks proved fatal and the decision was made to shut down the super calculator (quite possibly by Aelita herself).
 * As cool as that theory is, it doesn't quite work timeline-wise. The supercomputer was shut down for nine years, and Jeremie was twelve when he first discovered it...

Odd and Love Momozono are related. More likely cousins.
Both are blonde, both are lively and chirpy, and Love acted like a cat in episodes 14 and 15 of FPC, while Odd's Lyoko avatar just happens to be a kitty-boy. The reason for them having different surnames was that Ayumi (Love's mother) and Odd's father were siblings, and once Ayumi married Kentarou (Love's dad), she took on his own surname.

Similarly, William and Setsuna/Eas seem to have connections: both have black hair

Odd's affinity for purple and his flirty attitude might be caused by the excessive number of females in his family.
Seriously, having a mother, five sisters, and (referring to the Love theory above) a female cousin (no, Aelita does not count since she was pretending) might just influence him. And make him want more.
 * It could also be argued that his five sisters have led to his Casanova Wannabie tendencies. He mentions that they bully him (e.g. by locking him in the bathroom all night) and have complete control over him due to being older. Thus, when Odd is away from them at Kadic, he decides that he wants to be the one in control instead, and thus dates every girl he can to try and assert his control and sense of confidence.

The World is a Simulation
The "Real World" is actually a simulation like the Matrix (or is the Matrix), and Lyoko is a simulation inside of a simulation, or perhaps, a different layer of the same one. This would explain XANA's ability to seemingly violate the laws of physics. It also explains the Return to the Past: a type of loading of a saved state (or backup as it may be), but those excepted from it overwrite their old selves. Could also be why Jeremy's hacking is so effective at things which would seem to have other checks and balances (like Aelita's identity).
 * But if the "Return to the Past" works by restoring a "back-up" of the world, then why do dead people stay dead?

Aelita's personality completely changed when and because Franz Hopper restored her memories.
The Aelita in Seasons 1 and 2 and the Aelita in Seasons 3 and 4 are two completely different Aelitas, because a new Aelita was created when Franz Hopper gave her memories back. As a blank slate on Lyoko, Aelita was probably closer to the definition of an artificial intelligence- or maybe simply an amnesiac. She shows marked traits- an overactive martyrdom instinct, a demure, naive personality (though this does evolve slightly due to outside sources), and, for the little time she knows about her parentage before the memory restoration, acute hatred of her father.

My best guess is that when Franz Hopper restored her memories, he also restored a bit of her previous personality, and maybe a bit more humanity. She becomes noticeably more outspoken, she takes many risks both physically and socially, the martyrdom instinct vanishes (maybe because of a renewed sense of dignity?), she receives different powers for no apparent reason (this I think is the big one- because her brain changed, the makeup of her Lyoko form changed as well. The energy balls could be symbolic of her assertiveness...or uh something.), and, big one, she absolutely adores her father. Aelita wasn't replaced, because she has memories and all, but she was definitely heavily modified.
 * Reminds me of another extraordinary girl whose personality shifted towards the assertive halfway through the story. You sure Aelita isn't a half-Esper?

Jeremy is Haruhi.
He probably created all of Aelita's past and a way to bring her to the real world because he was really in love with her, and it'd be troublesome if she didn't come to reality, like he wanted. The change in personality was because it was how he imagined her.And XANA's Game Breaker status was just a way to keep away from the massive boredom. He probably created this new Universe after Haruhi saw that there was a game so awesome she wished it was real. Lyoko is this game.

The Men In Black aren't with the government, but with Smart Brain.
Antea and Aelita are Flamingo Orphenochs, whose cellular degeneration issues were fixed by Franz using Project Carthage and/or Lyoko (an independent project to break Smart Brain's status as leading Mega Corp by making their superhumans beholden to someone else besides the Orphenoch King for their gene fix). No word yet on how involved Decade has become in "Lyoko no sekai."
 * I have absolutely no idea what you just said. Keep up the good work.
 * If Smart Brain is involved, does this make Code Lyoko set in Faiz's world, Decade AR Faiz's world or another entirely? Plus, aren't orphenocs almost always grey in colour?

A crazy, yet plausible theory to Odd's Lyoko form.
The night before he enrolled at Kadic, he read the original Alice in Wonderland book before sleeping. Then, he dreamed about Kiwi peeing on a random log, where the Chesire Cat was resting. Kiwi and the Chesire Cat then started fighting... and then Odd woke up. Hence why in Lyoko he is dressed as a purple cat with a picture of Kiwi peeing as his Chest Insignia.

Yumi grows up and becomes Yumi Azusa.
She eventually moved to Death City, and somehow became a weapon and decided to enroll in the DWMA. I mean, look at her. Azusa dresses similar to Ishiyama, the hairstyles are fairly similar.. as for the last name, it could have been her mother's maiden name that she decided to take, and the reason she's called Azusa most of the time is because her father named her Yumi and she now has a grudge against her father like Maka does. She never mentions Lyoko because, well, she has to keep a secret.

XANA possesses humans because he enjoys taking human form.
It's the best explanation we've got. When he first possessed a human (Sissi), he made a comment in her body that he had "never felt so good." Perhaps over the seasons, XANA developed a liking for, or even an addiction to taking human form for some reason. This is why he did so, again and again, even after it was long established that this method did not work. He took William as his slave in Season 4 in order to have a human to possess whenever he wanted.
 * One dreads to wonder what would happen if he ever possessesed a girl permanently as well (he has been shown to spectre-possess multiple people at once, so there's precedent.)
 * He did. See the novel series.

Ulrich's real parents are Kyon and Haruhi
Got the idea from a since-removed Youtube video saying that kyon and Haruhi are Ulrich's parents due to Ulrich being a slight expy of Kyon and other reasons. Haruhi just transferred the baby to the stomach of a French woman. She IS god, after all.
 * If the baby wound up in her stomach, wouldn't that kill him before he was born?

Jeremie is Jeff Andonuts
Both characters are very smart for their age and are great with technology, not to mention they both have a similar hairstyle, blonde and wear glasses.
 * Flaw in your theory: Michel Belpois and Dr. Andonuts look and act nothing alike.

Aelita is a suicidal, Death Seeker
Think of all the horrid stuff that have happened to her. Think of the lack of therapists. Think of her.

Xana was never corrupted
Xana was doing exactly what it was programmed to do: destroy Project Carthage. In order to do that it needed to leave the factory. The program was merely protecting itself when it trapped Franz and Aelita Hopper and was continuing to protect its mission for the entire series.
 * That's not a bad theory. It makes sense. Perhaps the reason he created all those extra super computers was because he needed extra power to destroy Carthage (and he created those robots to defend the computers should they come under attack). I mean, since the Carthage was started (in what, the '70s?) it had probably grown exponentially. Hell, depending on just WHAT it does exactly, it may be a threat to the entire world. Heh, it's probably some sort of system that keeps the entire world under the control... What was that theory regarding The Patriots again? If this is all true though wouldn't that make Xana the hero of the show, which is nothing but a bunch of Nice Job Breaking It, Hero moments?
 * Or perhaps he already destroyed it at some point in the past and, as a result, decided to destroy the ones who created it, the humans, as an extention of the original programming.
 * So XANA is Helios?

Xana actually trapped them in a different bubble simulation at the end of ghost channels and they just think they are in the real world

 * Odd and Ulrich were right in temperary insanity.

XANA is 4chan!
The site has gotten self-aware and all the attacks are actually epic trolling! XANA is sitting on his throne of CP and laughing at them, thinking they destroyed him, but 4chan is still up! That means 4chANA is waiting, then will do an epic troll move and mess with their ego, by sending a giant Pedo Bear to attack them!
 * He already did that, in the first episode: "Teddy Godzilla".

XANA thinks that Yumi is the strongest Lyoko Warrior
It would explain why she's XANA's Designated Victim, after all. And there's some evidence to suggest that she is the strongest, at least emotionally - being a year older, she's naturally more mature and headstrong than the others. She's also had the most experience with the supercomputer other than Jeremie and Aelita (by season 4 she can perform Returns to the Past without guidance). And her performances on Lyoko are generally impressive as well. She's managed to beat William single-handedly at least twice, and she's the only one to have defeated Aelita whilst she's under XANA's control. All that added together explains why XANA goes after her so much - he reckons that if she goes, the others will be severely demoralised, and it'll be much less difficult to put them down as well.

Hiroki is adopted
Think about it. He's nowhere to be seen in all of season 1, even on occasions where he really should have been, such as in "Holiday in the Fog" when Yumi's family were going on vacation. This is because Hiroki isn't Yumi's biological brother, but instead he was adopted by the Ishiyama family sometime between "False Start" and the beginning of season 2.

Replikas are XANA's equivalent of Horcruxes
Jeremie's assumption (which the show then takes for granted) is that if all of the Replikas are destroyed, XANA will die as well. However, here's a different theory - although XANA is free from the Supercomputer, he still has certain limitations based on his core programming. That means that he still needs towers to attack the real world, and so he began usurping other supercomputers to create new towers to do just that. However, in the act of usurping each supercomputer, XANA left his core programming increasingly exposed, because he'd have to siphon off some of his power to create Replikas, much like how Voldermort had to split his soul and siphon part of it into his Horcruxes. This means that destroying the Replikas wouldn't destroy XANA totally, but instead they'd leave him much more exposed to a final attack. That's how Jeremie's multi-agent program destroyed him - it targetted all of the Replikas simultaneously, and once they'd all been destroyed, the program launched a final attack on XANA itself, killing him for good. If the Replikas had simply been destroyed and the Supercomputer shut down, XANA would still 'exist', but he wouldn't be able to do anything until he usurped another supercomputer.

Code Lyoko will reset it all
Every time they use Code Lyoko, they get sent back in time. One day they might get sent back to the beggining of all creation.
 * That presumes a lot about the RTTP's range. It might simply not have the power to send everything back THAT far. Though I wouldn't put it past the Warriors to pull a Mighty Max (Resetting back to the time of Xana Awakens) as a last resort...

William is a fan of Final Fantasy VII
Which is why his Lyoko Avatar is based on Cloud/Zack.

Ulrich has dyslexia
Ulrich is often shown doing badly on his schoolwork, frequently getting 'D-' or 'F' grades. Yet when Ulrich is with his friends and fighting XANA, does he seem unintelligent to you? My theory is that Ulrich is actually fairly intelligent - not to the same extent as Jeremie and Aelita, but still quite smart. However, because he has dyslexia, he has difficulty in reading books and writing essays, thus leading to his bad grades. The problem is that no one else has noticed that Ulrich is dyslexic, and thus slates his poor schoolwork as being down to laziness and a refusal to study. For instance, when Mrs. Hertz is chewing him out in "Nobody In Particular", he apparently wrote that a nucleus was made of "croutons" rather than "protons". Perhaps he did know the right answer, but due to his dyslexia he ended up writing a different word. Likewise, when another teacher slated his essay in "Double Trouble", the main critique was about the multiple spelling errors. Unfortunately, Ulrich is too shy and embarrassed to talk about his problems, even to his friends, so he doesn't get the help he needs. Remember how reluctant he was to admit he had vertigo? Frankly I'm surprised that it took me this long to consider this possibility...
 * There's a simpler/alternate explanation for Ulrich's bad grade's... having Odd for a roommate.

There are multiple XANA-esque programs across the world
While the gang are fighting XANA from Lyoko, and eventually delving into the internet itself to destroy supercomputers that the gang has taken over, there are multiple different groups fighting rogue computer programs just like XANA all over the world. Naturally, none of these groups know that any of the other groups exist, and so continue to fight computer programs in their respective virtual worlds in countries such as the United States, Australia, United Kingdom, China etc., basically every country that has powerful computers at their disposal. In the first two seasons, shutting down the supercomputer would only have removed XANA from the picture - the other rogue computer programs would still threaten the world's safety. Franz Hopper is aware of this, and so he sent data to Jeremie about all the other self-aware computer programs that existed. Thus, in "Fight to the Finish", Jeremie's multi-agent program was so powerful that not only did it destroy XANA, but all the other computer programs as well.

Lyoko is Franz Hopper's Minecraft world
Several years into the future (from the show's perspective), Hopper bought Minecraft and discovered the issue of lag when using too much TNT at once. So what did he do? He built a supercomputer that would allow him to blow up as much TNT as he could ever want. After a while, he got bored and added more features to the computer, including the ability to enter a read only version of his world and, for some reason, go back in time. After getting bored with that, Hopper made several mods that, among other things, replace the mobs we all know and love with more science fictiony mobs, make the world generate differently, cause falling into the Void to be more punishing, and, due to the computer's massive amount of power, add towers that can affect the real world with the right redstone sequence. And after a while, he used the computer to take it all back in time to the 70s where he settled down, got a wife, and eventually got his daughter so addicted to Minecraft that she went into the world and refused to leave. Consider these similarities:
 * The wirey cable thingies that lead to the towers are comparable to Redstone Wire.
 * The Digital Sea acts similarly to the Void. Instant death, loss of all data.
 * The four main Areas (desert, forest, ice, mountain) are comparable to the major biomes in Minecraft.
 * Carthage, likely the last thing Hopper built, appears to be made completely out of Lapis Lazuli blocks.
 * XANA, given all that he does, could be compared to Herobrine accessing towers allowing him to screw with people in REAL LIFE.
 * Replikas are worlds separate from Lyoko that Hopper made while testing his world generation mod, mainly to make sure each biome still worked properly.

So what it comes down to is this: Jeremy and the gang found this super computer, discovered Hopper's still Minecraft addicted daughter trapped in Hopper's world. The so-called "materialization code" was really a way to forcibly remove Aelita's addiction, allowing her to get out. Over the course of the series, the team goes and fights against Herobrine to keep him from screwing with real life in addition to just Minecraft.

Finally, Jeremy reveals that his hair is dyed, moves to Sweden, changes his name to Markus Persson, grows a magnificent beard, and makes a game called Minecraft hoping to one day make a less hostile but still with a fun amount of danger version of Lyoko that he and his friends can one day explore once more. He made Herobrine in an attempt to have something similar to but not as deadly as Xana, but removed him at some point after Franz Hopper went back in time, which was also before the Nether update. Endermen were his second attempt, but failed because they weren't sinister enough. Oh, and Ulrich went with Jeremy and took the name of Jen Bergstein.

In Code Lyoko: Evolution, Sissi will have a Lyoko form.
Why shouldn't she, now? Also, evolution makes me think upgrade, including in character ages. If they're older, they should have become closer, so why not let her in? If she does get one, I think it will be a Zelda/Sheik type deal. The Lyoko form represents your inner desires, don't you think Sissi would totally be a princess in that form... But it has to be combat ready, making me think that it will be like Zelda and Sheik.
 * And then she'll get turned evil, because the Warriors really can't catch a break.

Franz Hopper gave XANA a virus at the end of "The Key"
As we all know, at the end of "The Key" XANA managed to escape the supercomputer by stealing Aelita's memories, and Franz sacrificed himself to bring Aelita back to life. However, what wasn't shown on-screen was that while Franz was giving his daughter back her memories, he was also implanting a 'bug' inside XANA's core systems as he was escaping Lyoko. Throughout season 2, XANA maintained a link between him and Aelita so that if he died, Aelita would too. In this instance, however, Franz turned the tables on him, and the bug made it so that if Aelita died, XANA would be destroyed as well. This would explain why XANA never tried to kill Aelita throughout seasons 3 & 4, even though he's tried to kill the other Lyoko Warriors - doing so would lead to his own destruction. This also explains his actions in "Hot Shower", and indeed why he wants Aelita imprisoned within the Digital Sea - if she was trapped in the Network, then technically she'd still be 'alive', but completely unable to do anything. Thus, XANA wouldn't have to worry about the one key threat to his existence, and as soon as Franz Hopper was out of the picture, victory would be almost guaranteed.

Every episode after "Ghost Channel" never actually happened
In "Code: Earth", Aelita is finally materialised onto Earth, and in "False Start" she spends some time on Earth before being forced back to Lyoko. Then in "New Order", Aelita lives on Earth with everyone else. Well, that's what the show tells us anyway. In fact, every episode in the series except for the first 24 is merely a hallucination on Jeremie's part. On that front, so is the scene in "Frontier" where he touches Aelita's fingertips. What really happened is that XANA succeeded in one of his attacks for once, killing many people in the process. The gang realised that they could not handle XANA any longer, and reluctantly shut down the supercomputer. Jeremie, distraught by the loss of his one true love, even if it did happen to be a computer program, went completely insane and began hallucinating that he had finally managed to materialise Aelita (hence "Code: Earth" and "False Start"). Everything else that happens afterwards consists of further hallucinations from Jeremie - Aelita being able to live on Earth full-time (Jeremie's biggest dream), the revelation that she's human (thus making Jeremie's love for her less 'pathetic') and everything else... all of that is imagined by Jeremie as he lies in his bed, his friends having long since abandoned him, and the episode "Echoes" represents Jeremie regaining his sanity and letting go of his delusions.

There are two Aelitas
To be specific, the first Aelita lasts from the start of the series until the episode "Just In Time", when she's deleted. When the gang materialise the hair that was materialised, the implication is that it's the same Aelita. However, if you listen closely, you'll notice that they mention that the hair 'recreates' Aelita's code, rather than 'restoring' it. In other words, they made an exact copy of Aelita, with her memories intact. Now, at the time there wasn't much distinction, with her being assumed to be an AI and all. But this essentially means that the Aelita that went through so much Character Development, discovering her past and fighting XANA all the while, was not the real Aelita at all, but a computer-generated clone of the original Aelita.

XANA is a Knight Templar
For all intents and purposes, the show paints XANA as a Complete Monster, whose exact motivations remain unknown throughout the four seasons. However, a very distinct possibility is the idea is that XANA is a Knight Templar who holds a very firm belief that Humans Are Bastards. During season one, the only way he sees of removing their bastard-ness is to eradicate them totally. However, after season two, his motivations change as he grows in power - now, he instead wants to become powerful enough to possess everyone on Earth, and manipulate them in a way that he believes will 'benefit' the rest of the planet. This explains the robots we see late in season 4 - perhaps they are designed to get rid of anyone who manages to resist XANA's possession. More importantly, it explains why possessing humans is by far XANA's favourite method of attack, despite the fact that it has failed to produce results multiple times - he wants to stay in practice for when he's finally strong enough to possess millions of people at once.

The Supercomputer was Sailor Pluto's PC
And she built it herself, adding the Time Travel function and the holographic part out of boredom (she has literally nothing to do for a long time). Also, she powered it with plutonium to keep herself entertained when she had to recover the fuel. Then she grew bored with it too and hid it near Paris, where Franz Hopper found it.

Jim Morales does not age
This would explain the bandage, the five-o-clock shadow, and how he had so many previous jobs on top of working at Kadic Academy for 20 years. He also never mentioned the real reason he was embarrassed about Paco, King of Disco. It could have been made a long time ago, but Jim still looks about the same.

Mr. Puck's appearances in Aelita's dreams are a mental defense mechanism.
Besides the fact that some of her memories were removed from her and stored in Lyoko, she also partially repressed some of them. Mr. Puck is a mental avatar for Aelita (also helps explain why her Lyoko form is an elf), and she remembers herself as Mr. Puck in order to avoid confronting har traumatic memories directly.

Odd is Self-Abusive
Think about it. I can't offhand think of any real episode where Odd wears anything less than long-sleeved outfits. Ulrich knows, which is why he never complains about Odd hanging off of him. He mentions that his sisters abuse him in the most nonchalant of tones, and doesn't seem surprised when a girl pulls something particularly nasty. On another note, William also knows, but doesn't say anything.

William is related to X.A.N.A.
William was the most easily possessed of the six, and having a genetic relation could be X.A.N.A.'s 'back door' into William's mind.