Assassin's Creed/WMG

The final lead-in to the present-day installment will take place in the 1960s
The Templar-controlled CIA and FBI will be major players, and one of Desmond's immediate family (father, grandfather, uncle, cousin, take your pick) will be the player character. The Templars' and Assassins' involvement in the Cold War, the career of J. Edgar Hoover, the Bay of Pigs invasion, the Vietnam War, and the CIA's wars against communist regimes in Central America will all be explored. The player will use cutting-edge technology to assassinate Russian and American spies involved in cloak-and-dagger operations in major American cities, ultimately trying to avert nuclear war by taking out a major historical character. Naturally, the game will culminate in President Kennedy's assassination at the hands of the Templars.

All Those Who Came Before were closest to the ancient Romans.
This explains a few things:
 * Why are in Rome (in close proximity to the ancient city no less),
 * Why the Ones Who Came Before we meet have names of Roman goddesses (Minerva and ).
 * Why their characterization matches with their roles in Roman mythology:
 * Minerva seeing into the future to Desmond, and

Assassin's Creed III will be released in September 2012.
Just so it can perfectly match the in-game time.
 * Well Ubisoft seems to be trying to get one game out a year, so this all but confirmed.
 * It is. They outright stated it'd be pointless to do the whole "save the world by December 21, 2012" thing if it's already past that deadline IRL.
 * Jossed. It's coming out on October 30, 2012. Close guess, though.

A Fission Mailed will happen sometime in the series.
Either as a glitch in the animus or whatever, but either way, it could happen.

Altaïr and Desmond are the same person.
The Apple let Altaïr cheat death by reincarnated as the person we know to be Desmond. This explains why Altaïr looks exactly like Desmond, and why he carries the same exact scar. This also lets Altaïr use the apple and not turn out to be a villain.
 * Except that it's pretty much established in the first game that Desmond looks exactly like Altaïr because the Animus is letting Desmond impose his face over Altaïr's in order to make him more comfortable in the Animus...which pretty much means we actually have no idea what Altaïr "actually" looks like.
 * And Desmond and Ezio don't look exactly the same because Desmond is far more used to using the Animus, and the Animus 2.0 is superior to version 1.0. This allows Desmond to not have to impose so much of his face over Ezio's. Which is why two look simply similar, rather than exactly the same...but we still technically don't know what Ezio "exactly" looks like.

Ezio has untreated Chronic Backstabbing Disorder.
His condition may have started out mild, then snowballed into what it is during Assassin's Creed II, namely, stabbing every guard who tells him to get off the roof. Mileage is gonna vary on this one, since it kind of depends on how one plays.
 * Why bloody my blade, when there's a perfectly good unsurvivable drop nearby?

Assassin's Creed: Brotherhood is really Assassin's Creed III in disguise!
Why would Nolan North sign onto a game he would have a bit part in?
 * Money Dear Boy.
 * Plus contract obligations.
 * He was told he wouldn't be typecast.
 * Semi-confirmed? This official video (jump to about 1:10) tells us that Desmond will appear, but not in what capacity.

Durandal, Joyeuse and Curtana/Cortana (same Sword, different spelling) are all POEs.
Excalibur was a PoE, and there were many Apples, so why not swords? They are all legendary swords (who's names have been used in gaming before), and they could all Pieces of Eden. Durandal was also indestructible, and was forged from the same steel as Cortana and Joyeuse.
 * Swords aren't the only legendary weapons out there. Plenty of staves and spears have worked their way into myth and legend. Since we know at least one POE was a staff, there could be others out there as well. The Green Dragon Crescent Blade wielded by Guan Yu, the Ruyi Jingu Bang wielded by Sun Wukong, the Spear of Longinus...we could go on forever.
 * If we're talking about legendary swords being PO Es, I like to think Kusanagi is one too.

Mass Historical Templar Guessing
Well, lets start coming up with plausible historical Templars. I'll start: Abraham Lincoln (assassinated by the assassin JWB, perhaps the Top Hat was a Piece of Eden), Bill Gates (Still Alive, POE: Unknown), Tim Burton, meant to keep the masses entertained, stopped but not killed by the Assassin JS (killer of Batman Movie Franchise, Note, Burton fan, but this is WMG), The Founder Of TV Tropes (not sure of his name). His POE is this website (the effects are... similar).
 * Barack Obama. He's going to convince everyone to give up their individuality in the Assimilation Plot. POE: Unknown.
 * Shigeru Miyamoto. Because he's been running the video game industry from behind the scenes since Donkey Kong came out. POE: The Nintendo DS. The money it prints? IT'S AN ILLUSION! And he's able to pry into the POE and change its appearance every few years, leading up to it now being the prototype Nintendo 3DS. Its visions also inspire his games: he doesn't need Super Mushrooms to make the next Super Mario Bros, he has a Piece of Eden!
 * Joss Whedon. Keepin' the nerds from knowin' the truth by entertaining them till they are his personal army. POE: The apple can "enslave" people right?
 * Oh hell, what's the point? If you can name someone, they're a Templar (if not, they're an Assassin).
 * Gene Roddenberry: Totally an Assassin.
 * Guy Fawkes: Also an Assassin.
 * No, he was a Templar. He was a devout Catholic and the Catholic church was run by Templars(he even fought in Spain for the Catholic side), and his goal in killing King James was to put a Catholic monarch on the throne so that the Templars would have more control over England. It had already broken away once from their control.
 * Hammer Fall: Blatantly Templar propaganda. Vidic probably had "Bring The Hammer Down" playing when he raided the Assassins' hideout.
 * As heavily implied by this Cracked article, Ehud of The Book of Judges.
 * Marx was an Assassin, Lenin was a Templar. Marx developed the philosophy of communism as a counter to (Templar-developed) capitalism. Unfortunately, the Templars used Lenin to corrupt communism and create dictatorships.
 * Oda Nobunaga was a Templar and Akechi Mitsuhide was a covert Assassin.
 * Todd in The Shadows is an Assassin who is against the Templar-run music industry. I mean, sure, his hoodie isn't white...but he constantly wears a hood! Like an Assassin!
 * Obviously Bill Gates has the Apple, hello?
 * Wouldn't Steve Jobs make more sense?

MODULE-32A:

 * First, there's the provenance of the crazy relics Abstergo is interested in, needless to say; they mention a "Christ-figure." My guess is that this is probably Jesus Christ, obviously; he wasn't so much miraculous or the Son of God as in control of these items. So...alien relics, perhaps? Also, maybe someone can submit the text pyramid and text rectangle to cryptanalysis; I didn't get the rectangle, or the square, but the pyramid...

Formatting issues, of course. Sorry about that, but...

a drh oodtm whbitdo eusysinse aroomyeaynr iseytnidlmide twihnyieaudaght

I'm also not sure how well I interpreted the text; scrawled with blood on concrete, then washed away does not for legibility make. I think that the messages had something to do with the Subject 16 you read about on the terminals.
 * With the rectangle, start at the bottom right corner and read up. It takes a while to decipher and it helps if you write it down. Off the top of my head, the message is "they take my mind to make their plans, I spill my blood to show you the truth" or something similar. The triangle is read the same way and discusses the Templar plans to launch the piece of Eden into space to take over the world. I think.

(Sorry if I screwed up somehow and this already exists.)

The mysterious female Knight Templar is related to the meta-plot's Lucy

 * So I'm not the only one who thinks this: the physical resemblance is uncanny. Maybe after Altaïr spared her life she dedicated it to finding out more about the assassins and realized they weren't so bad after all.
 * According to Assassin's Creed II it seems that she's the mother of Altaïr's child, so she's related to Desmond. Not so bad indeed.

The mysterious artifacts are actually from the future, they got sent back through time travel
So, Twenty Minutes Into the Future, The End of the World As We Know It occurs. Lucky for us, someone is able to send powerful artifacts back in time that hold the key to stopping this disaster. In order to ensure that they survive long enough to be used come 2012, the artifacts are disguised as holy relics. So, we have one that looks like an apple, and it can deceive people, we probably have a spear similar to the Lance of Longinius, and so on. Somewhere along the line, the Templars mistakes these artifacts for the real thing.

Furthermore, they give up on finding any relics involving Jesus. This will backfire badly as the "Holy Grail" will obviously be the... Holy Grail of all these artifacts. Desmond is going to find it and save the day at the end of the series.

Evidence of the time travel presents itself in the final scene of the animus. The "piece of Eden" shows a map that distinctly outlines all the modern-day countries. The Precursors would have no way of knowing that. The fact that the Creediverse is an alternate continuity to our present day comes when Dr. Vidic says "Some of the artifacts are on land masses that no longer exist." ~ All the land masses I saw sure seemed to be there today.
 * The world is in fairly the same shape as it was then, with some exceptions, mainly around islands and coastlands. Alternatively, it's a projection of the world as it was in the 12th Century. Islands can disappear in that time.

Desmond is already a trained Assassin.
Desmond was on "the farm" until his teen years, and obviously, there was no attempt by his parents to hide their status as assassins. Ergo, Desmond must've started training as one, even if he cut and run long before he would've gotten to Altaïr's level. He doesn't need Altaïr's memory leak to be an assassin, only for Altaïr's sixth sense; he already has the basic skills, perhaps marred only by disuse.
 * It's stated in the game that he is, multiple times. He says he's not an assassin "any more", why else would the assassins try to save him?
 * Does this mean that the last installment of the game might have you play as Desmond?
 * In the second game, Desmond really has no assassin training whatsoever. However, reliving Ezio's life via the Animus allows him to acquire years of training in just a matter of days.
 * Desmond repeatedly says he "was" an Assassin, but isn't anymore. Perhaps he is a trained Assassin, but just wasn't trained in the more physical aspects of it that involve dicing people up, Altaïr and Ezio style. Maybe he was training to be an analyst-type, versus a field Assassin. Or, considering how often it's mentioned that present-day Assassins are pretty weak, at least in relation to the financially and resource rich Templars, the Assassin group Desmond came from may be some splinter cell of super paranoid, cult-like Assassins; they know that they're fighting Templars, but they weren't aware of just how powerful a force they were fighting. Which is why Desmond is totally ignorant about how far back the battle between Templars and Assassins goes and doesn't have the physical training to handle them. Being in the Animus and reliving his ancestors memories simply opened his eyes to the truth.
 * The events of Assassin's Creed: Revalations puts this all to rest,

Lucy is not an actual Assassin.
Lucy is noted to have spent a large amount of time working on her education, enough that it would've precluded her from secretly being a part of a clandestine organization. If she were an actual Assassin, she wouldn't have built the Animus for Abstergo anyway. More likely, she decided on her own that Abstergo needed to be stopped, and in choosing to take action, she became an ally to Abstergo's enemy: by default, the Assassins.
 * The second game pretty much confirms that she's an Assassin.
 * Although it's possible she's not of an Assassin bloodline, as is the case with Shaun people can join the Assassins without being a descendant.
 * Not all Assassins go around murdering people a la Altaïr, Ezio, and . While she has some basic skills, her real usefulness to the order is in the use and operation of the Animus.
 * E-mails and dialogue in Brotherhood state that both Rebecca and Lucy were "chosen" to be part of the Assassin order. The only one in their team that was born into the order was Desmond.
 * Confirmed but Subverted: Lucy was chosen to be an Assassin but later

The Assassins' who assaulted Abstergo succeeded.
Assassins are masters of blending in; if they won the engagement with Abstergo security, they would've planned ahead of time to impersonate them. Notice that the voice telling Vidic all is well seems to be different then the one reporting the situation minutes before. If the Assassins are as low in number as Vidic says, surely they never would've entertained the possibility that a direct assault on a security-filled corporate headquarters would work, and would've planned from the get-go to use subterfuge. This is why Lucy is so confidant that Desmond will be fine if he just trusts her; she knows the cavalry is here and they're just waiting for the Templars to turn their backs in their excitement to sneak him out.
 * Possibly Jossed by Assassin's Creed II - Lucy is the only person that helps Desmond escape. However, it was pretty easy for them to escape such a secure facility...
 * New WMG: they didn't succeed, but they killed most of the security personnel.
 * Jossed: According to the Lost Archive DLC: It was planned out by and

The new security guard is an Assassin.
The manual makes reference to a new-hire security guard in charge of monitoring Desmond through the cameras. Consider the amount of sneaking around Desmond is able to do thanks to Lucy leaving him the door-lock combination, and the fact that she would leave it at all, knowing there are cameras in every room. Neither Lucy nor Desmond are ever busted, and the "new security guard" scenario in and of itself just reeks of Chekhov's Gun and/or an Untwist. It would also add more credence to the above.
 * Lucy mentions that she hacked the cameras, but could have done it with help from the new guard.

The Assassins are not extinct.
Abstergo has gone and enacted their own personal Order 66 against the Assassins as best they can, but the Assassins who attacked the corporate building weren't the last. Rather, the Assassins have taken advantage of their depleted numbers to let Abstergo think that they're no longer a threat; the Assassins are heavily disadvantaged in manpower and resources, but if Abstergo thinks there aren't any left, it gives them the element of surprise when they make their next move, probably a very carefully planned one. It's an advantage they've practically never had, since the Templars have always known they've existed. The Templars may well and truly fail at handling a situation involving supposed-to-be-dead Assassins so badly that it makes all the difference.
 * This would fit here if it wasn't blatantly stated in the emails.
 * Protip: Those emails were written and sent by the Templars. If the Assassins are deceiving the Templars, the Templars would naturally be convinced that the Assassins are extinct.
 * Pretty much confirmed in the second game. The Assassins are still around, but aren't nearly as powerful as they used to be.

Adam and Eve were the first Assassins
Mostly from their parkouring, of course, but it would fit if they (or their descendants) founded the Brotherhood. Alternatively...
 * Well, it is confirmed in one of the first Subject 16 puzzles that Cain, their son, is the first Templar. So perhaps the great irony is that the Templars are descended from Assassins? So all this time, the whole Assassin vs. Templar thing is really a true civil war since they're all related and can trace back their ancestry to Adam and Eve?
 * Since Cain is a Templar and killed his brother Abel, perhaps Adam and Eve's biblical third son, Seth, took it upon himself to kill Cain in revenge, making him the first Assassin?

Adam and Even founded the Assassins AND the Templars
If the biblical passage is taken metaphorically in in-game terms, then Eve was the one that really wanted the Apple, i.e. the precursor supertech, and Adam was more along for the ride. It could be that in the "real" story their story had less amicable conclusion after their cast-off from Eden (Adam wrested the apple from Eve, or vice versa for example).
 * Jossed: Their son Cain was the first Templar. They gave it to Abel, but Cain would have none of that now, would he?

Subject 16 has that video because he's BEEN either Adam or Eve in the Animus
And how they tried to hide those uncomfortable origins is part of why they made him go crazy with Animus overuse.
 * More or less confirmed in-game: the screen at the beginning of the video reads "Subject 16 - Session 12: [Date Classified] B.C.E."
 * He was neither, keep in mind its not a video of some random over the shoulder camera following Adam and Eve, there's a 3rd person chasing (or following) Adam and Eve, and said person is Subject 16's Ancestor, we are seeing that "video" from Subject 16's POV
 * Then maybe Subject 16 has been Lilith, the only other human around back then.

Since most of the Assassins share a bloodline, Subject 16 has been Ezio, too!
That's one explanation of how he planted his videos around all and only the places that Ezio would visit. This would pose quite a few problems, of course.
 * Alternatively, 16 has been another assassin that knew Ezio, but not Ezio himself.
 * Or more simply, 16 never hid the files around Italy, just programmed the Animus to hide them in any important landmarks that anyone who uses the Animus would visit.
 * It's stated in game somewhere(Don't remember, sorry) that Subject 16 favored Renaissance Italy.
 * This is canon if you actually play through the opening of Assassin's Creed II. Lucy asks Desmond to get into the Animus before leaving the Abstergo facility in order to track down an identical memory from both Subject 16 and Desmond. The identical memory they find is the birth of Ezio.

We've never seen Altaïr.
Sure, at first glance, Desmond is Altaïr's Identical Grandson. This does not, however, explain their matching scars. The Animus is merely rendering Desmond into Altaïr's place, visually, because Desmond is experiencing these memories as if he's there. We have no idea what Altaïr looks like. Sorry, ladies, the badass assassin doesn't have sexy scars, just the dorky bartender.
 * This is also stated very blatantly in the game.
 * Thrown for a loop, though, with AC2. Not only does Ezio have the scar (which would match with the above information) but we see how he gets it in the beginning of the game. So either people from Desmond's family have a natural predilection for ugly scars, or the Animus decided to rationalize Desmond's face.
 * Thrown even MORE for loops in Altaïr's Chronicles and Bloodlines, which don't seem to technically take place inside the Animus.
 * Confirmed with the release of a gameplay trailer from Revelations, where Ezio is the one reliving Altaïr's memories. He looks completely different.

We've never heard Altaïr.
In addition to the theory above, Altaïr's voice isn't his own, but Desmond's rendered in Altaïr's place. I mean, it's not like he'd actually sound like that as an Arab in the Holy Land.
 * This may have made sense if Altaïr's voice was the same as Desmond's, but Altaïr does have a different voice actor Philip Shabaz. And again, thrown for a loop with ACII where Ezio has a very distinct Italian accent.
 * Ezio's distant and more realistic accent could simply be the result of the combination of the superior programming in the Animus 2.0, and Desmond's ease with the Animus from using it so much, allowing him to be in way better sync with Ezio versus Altaïr.
 * Maybe the genetic memories have decayed more from Altaïr because he lived longer ago.
 * Altaïr did have an accent in Bloodlines.
 * Read an article on a website around the time of ACII's release, and it was speculated that Altaïr was given an American accent in the original Assassin's Creed because higher-ups were worried that American audiences wouldn't take to a blatantly ethnic (secondary) protagonist. Sadly, this may very well be the case. But luckily Altaïr will have an appropriate Arabic accent (by his original voice actor!) in Revelations.

Desmond's mother was Eva.
To explain Assassin's Solid: Desmond's mother was Eva, aka Big Mama, aka. This naturally means that Snake carries the same genetic memory as Desmond, because Eva's involvement in the cloning process means he is technically descended from Altaïr.

(And just for anyone who may not know; while that silliness was an obvious April Fool's joke, Altaïr's costume is unlockable in MGS4.)
 * Problem: Snake does not have any of Eva's DNA. Therefore, either the Japanese woman that donated the egg or Big Boss himself were descended from Altaïr.
 * It sure as hell would explain Big Boss, though.

Lara Croft will find the Pieces of Eden.
Just a note, I don't actually believe this but I think this would make a great fanfic!XD. Apparently in the new Tomb Raider games, there is no magic. "The ones who came before" could be referring to the Atlanteans in the Tomb Raider games. So the assassins ask Lara to retrieve the artifacts before the Templars do to save the world (again)! And the whole world being controlled by Templars for peace could be the Seventh Age. Oh and it could happen, Ubisoft is interested in buying Eidos so you'll never know. :)

Assassin's Creed is a prelude to the story of Ayreon.
The Animus is an early version of the Dream Sequencer.

Assassins are symbolically "married" to the Brotherhood, over and above their possible spouses.
Lucy and Altaïr are both shown to be missing their left ring finger, the same one that bears the wedding band in--at the very least--Christian tradition. The ritual removal of this finger could be used by the hashashin to remind its members who their real family is. Dem boys is crazy.
 * Considering that the protagonist of AC2 is a nobleman turned assassin from 15th Century Italy (which would mean he would probably be a Catholic prior to becoming an assassin), which would make this theory plausible. To add to this (or not), he has 2 hidden blades, meaning he severed BOTH his ring fingers.
 * Wrong on the non-WMG parts. Lucy was just holding her finger to look as though she was missing her ring finger as a sort of secret handshake, and Ezio still has both ring fingers (you can tell because he wears a signet ring on one hand) as a result of Leonardo Da Vinci's modifications to the hidden blade he uses.
 * In the mission where you get Leonardo Da Vinci to repair the hidden blade bracer Ezio's father had hidden away Leonardo says that he's going to have to chop off Ezio's finger. It turns out he's joking as the design has been modified to make it possible to use with all finger attached.
 * Altaïr's journal states that he implemented changes in the organization to keep up both with changing times and changing Templar tactics, the arguably biggest change being to phase out the more theatric practices, such as maintaining fortress-bases, making their assassinations public for the sake of turning themselves into Memetic Badasses, and severing the finger. As Altaïr puts it, the Assassins are their creed, not their ceremony.
 * However, in the Assassin Initiation ceremonies seen in AC2 and Brotherhood, new Assassins are branded on their left ring finger, instead of having it completely severed.

Everything Desmond was told about the Animus is wrong.
Looking through a persons life by reading their descendants "genetic memory"? A big case of You Fail Biology Forever. However, time travel is hinted to exist, and the Abstergo seems to have had access to technology that lets them mess with peoples heads, like the Piece of Eden. Its possible they combined those two things, and use the Animus to read the mind of someone in the past. They just use Desmond to lock on to his ancestor and the images Desmond sees are straight from Altaïr's mind.
 * Wait, reading the mind of an ancestor in the past is more plausible than genetic memory? I'm having trouble seeing how you can accept psychic time travel as an element of the AC world while rejecting genetic memory completely. This would also carry the unfortunate problem of turning all the Gameplay and Story Segregation from "It's an Animus abstraction!" into, well, Gameplay and Story Segregation.
 * Also, cases of Did Not Do the Research and "You Fail X" are covered in the plot: why do the marks, real people we can look up in an online encyclopedia, not die in the right way or the appropriate times? The Templars made up false history to cover up the Assassins' work. Why do we have technology? The Templars reverse-engineered stuff from Those Who Came Before and selected people to pretend to invent it. Why do we think Leonardo Da Vinci never got his flying machine working? The Templars deleted it from history, assuming anyone who would write it down heard about Ezio taking flight to begin with. Why does genetic memory exist when we "know" science has proven it's an impossible fantasy? The Templars and Pieces of Eden are responsible for what the public thinks science has and hasn't done. Is it a Hand Wave? Yes, but it's a very good one, because it's always consistent and an important plot point, not just a random Authors Saving Throw.

Humans don't have genetic memory
Those Who Came Before do, and they passed it on to the assassins when they interbred.

The deaths of the Templars did not happen the way you see them in game.
After assassinating an individual you get to watch their Final Speech as they lay dieing in your arms. However, if you hit the glitches you see them up and about talking to you. It seems like the assassinations didn't quite end the same way as you think and Altaïr actually spent some time discussing matters with his targets before killing them. This is supported by the female scapegoat, who you see bleeding from the neck only to revert to perfect health when Altaïr chooses to spare her at the end of the scene.

This seemed kinda obvious to me, but a lot of people seem to bring up how it made no sense for them to be talking to you for a few minutes after having been stabbed through the neck.
 * Not surprising, because the Animus is not 100% perfect, with the number of the times the simulation desynchronizes (depending how good/bad at the game you are). It's very likely that the Animus doesn't need an exact reenactment, just the fact that it was Altaïr/Ezio delivering the killing blow to the target.
 * This troper always assumed that it told the ancestor's story in Broad Strokes - everything happened, just not necessarily in that order or exactly how it is shown onscreen. This would cover a multitude of the Animus' sins.
 * Or, since the Animus is being run by Templars, they added in the speeches to make them look better to the person in the Animus. Would fit in nicely with how they don't have those long scenes in Assassin'sCreedII because.

AC II's equivalent of Robert de Sable will be Rodrigo Borgia
This is drawing from the "Lineage" movie. Rodrigo was the main villain, so he may assume Robert's role in this game.

Assassin's Creed and Rah Xephon take place in the same universe.

 * After playing through Assassin's Creed II we learn that there was a more advanced precursor race that had created humans in their image. Eventually they came to conflict and the precursors were wiped out while a calamity shook the world. This roughly matches up with when Bahbem tested his artificial god system, the Rah Xephon, and split the world along human and Mu lines.
 * The Pieces of Eden are actually Mulian technology that got left behind when the worlds were split. The Mulian mind control and illusions through out Tokyo Jupiter are powered by Al-Mualim's Piece of Eden, or tech derived from it.
 * Bahbem himself created the Templars. Most likely to serve three purposes. 1) To influence the world around him, 2) To find the Pieces of Eden and 3) Because he got bored waiting thousands of years for 2012 to roll along.
 * The Animus itself is also based on Mulian technology, most likely derived from whatever Bahbem used to transfer his mind into his clones.
 * By extension we can infer that Bahbem's process of transferring into clones is at least partially based on manipulating the Genetic Memory.
 * The reason Abstergo and the Templars are trying to kick off their Assimilation Plot in late 2012 is to get the world ready for the end of The Age of Katun. Bahbem would like to remove as many interferences as possible from his plans and directing most of humanity according to his whims goes a long way toward that. When things didn't go as planned Bahbem decided to scrap the idea and launch his Mu invasion plan instead.
 * Futagami is an Assassin himself, who decided to infiltrate the Earth Defense Federation and then TERRA to find out the truth of the Mulain war. His assassination of Bahbem was merely the final act in the millennia old feud between the Templars and the Assassins.

Desmond will be the protagonist of the next game.
Every vault location was revealed on Ezio's map, so there's no need to try and find them anymore, and Desmond is a trained assassin at this point, so all that's left is locating the remaining vaults and saving the world.
 * The developers have a pretty high stake in the meta-plot's ability to let them make games in completely disparate locations and times that yet still relate to each other. It's possible they may take the story in a completely different direction to continue doing so.
 * The Other Wiki says the developers were discussing possibly having a female ancestor around the time of World War II, going back to the time of King Arthur, or feudal Japan. While the protagonists of the meta-plot don't seem to have much time left to prevent The End of the World As We Know It, they can apparently speed through the entire lifetime of Ezio's ancestors in a few days, so it wouldn't be surprising if they squeezed a couple more out before Desmond springs into action. That said, I also remember hearing talk that they explicitly planned to make the games a trilogy, and with each new game comes a greater chance of Sequelitis or openly grabbing for more money...
 * Ubisoft could always wrap up Desmond's story in Assassin's Creed III, but continue on with stand-alone games, either featuring Desmond as the protagonist, or someone else (probably a woman).
 * The next game has been determined ala Game Informer's June issue (apparently they have a huge problem with leaks). AC: Revelations will feature all three Assassins (Altaïr, Ezio, AND Desmond)as playable and will take place in Constantinople at the height of the Ottoman Empire.
 * Jossed again. The protagonist of Assassin's Creed III is another one of Desmond's ancestors.

Desmond's Bleeding effect, and the entirety of the Animus Project is a Xanatos Gambit By Altaïr to gain Immortality by using the powers of the Pieces of Eden.
Codex File 30 explains how Altaïr was searching for a way to cheat death in his last days. He takes a final look into the Apple.. which tells him about how his consciousness can be given to another so he may live again. Desmond's hallucinations, etc, are Altaïr attempting to gain control of Desmond.
 * The obvious conclusion here is that Altaïr will turn out to be The Man Behind the Man and the True Final Boss of the last game.

People really weren't that annoying back then, Altaïr and Ezio were just misanthropes
In the first game, you were always getting shoved around by lepers and harassed by beggar women. In the second, you can't walk 20 feet without being accosted by every no-talent minstrel in Italy. No way people were really this annoying. Rather, since your experience is constructed from the memories of Ezio and Altaïr, you are seeing their perceptions of the world and how many annoying people were in it who just seemed to be out to get them in particular. In all likelihood Ezio just had one or two missions made far more difficult than it should have been by some Spoony Bard, but that experience was enough to sour his perceptions forever, and populate the streets of Florence in his memories with a veritable army of pushy troubadours.
 * Dude, have you ever BEEN to Italy? People really are like that there.
 * If the entirety of the experience is based on their perceptions instead of solid memory, they must've been very good at remembering the layout of each and every building in each and every city. You can't even say it's an effect of the Animus, considering everything looked just as detailed during the Bleeding Effect vision of Altaïr.
 * You'd be amazed what human memory is capable of storing. The human brain is basically a infinite-capacity storage drive, and it is literally impossible for a human mind to forget something once it's been set as part of long-term memory without suffering brain damage. Considering that Altaïr, Ezio, and the other Assassins regularly spent a great deal of their time running around rooftops and climbing buildings, and were trained (and probably genetically disposed toward) noticing and remembering things, it's not that surprising that they'd have excellent memory and awareness of the layout of the cities they worked in.
 * Arguably, the memories of the Assassin's aren't all that detailed in the first place. Perhaps Desmond is only aware of what details the Assassin's WERE aware of, with the missing details being written in either unconsciously or by the Animus. If you want to take this logic even further, it's not like you're aware of EVERY single little detail on your screen when you're playing the game, but your mental image still seems complete in every way.)

The Animus 2.0 deliberately amplifies the bleeding effect, or removes the safeguards in place to keep it from happening.
In the first Assassin's Creed, it takes the entire game for Desmond to gain even a small part of Altaïr's abilities. In the second game, however, Desmond, in what seems to be a shorter period of time than the first game, gains what appears to be all of the experience and abilities of Ezio. Therefore, it seems that the Assassins deliberately induced the bleeding effect rapidly in order to impart Desmond with the knowledge he needs in a very short amount of time. They did this either by removing safeguards that the Templars had in place to try to keep Desmond from gaining Altaïr's skills, or by deliberately accelerating the effect.
 * Either that, or the Bleeding Effect increases in potency exponentially. After a crack was opened to let the Eagle Vision in, the floodgates broke and Desmond became more receptive.
 * Lucy outright says that Desmond had become more receptive to the bleeding effect because he's already spent a decent amount of time in the Animus.
 * It could be that the Bleeding Effect is amplified due to Desmond's longer sessions in the Animus - he doesn't have any breaks between most of the Sequences like in the first game.
 * The fact that Altaïr's memories are much older than Ezio's might also have something to do with it.
 * This was explained in-game as Desmond learning the skills alongside Ezio, which is why we follow Ezio from the start of his 'journey' and not further down like we did with Altaïr.

Dexter is Subject 16

 * Similarities are discussed on the Dexter WMG page.

The Apple can send information through time
Altaïr's Codex in the second game mentions visions of the past and future obtained from using the Apple, and as mentioned above, this ancient artifact contains within it a modern day world map. Then at the end of the second game Either Desmond will find the Apple himself at some point in the future, or technology from the Apple was used in the construction of the Animus, allowing the necessary information to be passed back and causing a Stable Time Loop.
 * The visions of the future Altaïr sees are pretty much just the and the resulting destruction, something the Precursors predicted. It's not an actual vision, just a warning of what's to come.

Mario is related to Desmond
*Cough* I'll get my coat.
 * Alternatively, Desmond is a gamer and when he heard the name "Mario" in what is basically a video game he immediately thought of one thing. The Animus is known to convert language into a form that will be familiar to the user, and as a side-effect of this changed Mario's introduction into the very thing Desmond was thinking of.
 * Well, the first game's manual does mention that slackers have become much better with the Animus since Abstergo switched it to video game controls. And Desmond is so good with the Animus, so you may be right about Desmond being a gamer, which adds plausibility to this guess.

The Assassins are Not Quite Human.
So, how is it that Desmond and his ancestors have superhuman senses, can beat people to death with relative ease, and survive 40 story falls just by landing in some hay? Well, we know from AC2 that. Looking at one of the glyph puzzles, concerning, all the relevant clues to solving the puzzle involve paintings depicting. From this we can pretty easily infer that assassins are hybrids of some kind.
 * Expanding on this, it's not all Assassins, but just a select few lineages that are hybrids. This explains why the modern Assassins are so concerned with having Desmond learn the skills of his ancestors rather than just using one of their existing agents - the other agents are purebred humans and can't learn all the skills. Also it has the potential to explain away the scientific problems with the Animus - human DNA doesn't have genetic memory, but precursor DNA does.
 * Fridge Brilliance: Al Mualim's explanation about Altaïr and why he didn't use the Piece of Eden on him was "Who you are and what you do are too closely intertwined." But what if the reason he didn't use the Piece of Eden on him was, being a genetic descendant of Those Who Came Before, Altaïr's ability to be affected by the POE was limited? The POE could only create illusions that he could easily see through using Eagle Vision. Since normal humans are engineered to be receptive to POE illusions, Altaïr and the genetic Assassins may be less affected by the POE.
 * Al Mualim had no problems manipulating the other Assassins with the Apple. Altaïr probably has some sort of naturally occurring genetic mutation that allows him to see through the Apple's effects - one that was passed down to his descendants.
 * Alternately, Son of No-One isn't figurative, its literal; he was created by the last of the Precursors and left for the Assassins to find. His "parents" are nothing more than a wet-nurse and her husband, who were cast aside once he was old enough to begin training.
 * Explains Jesus being an Assassin and the Bible being factually correct. Also explains why Altaïr and Ezio can run around rooftops at the age of 60 or so, when the Life Expectancy was about 30.

Altaïr can swim just fine.
The Animus just has a glitch, as confirmed in the ACII manual.
 * Alternatively, Altaïr can swim, but he didn't at any point during those missions. Just as he didn't kill civilians, if you.

Desmond never left Abstergo
Desmond is fooled all along by both Vidic and Lucy. They both play around with his feelings and they have tried to make him more willing into this project by making Lucy 'betray' Templars and pose as one of Assassins to push him into phase 2. Notice that she's the one to disarm most of the security guards! Also she have put Desmond into car trunk so he could not see where he was taken but she never actually drove far from Abstergo if ever left the facility. And just have a look around new hideout. It look suspiciously similar to old one, just made a bit of retro style. And still you cannot have much of view outside, like it's very important to keep it from Desmond's knowledge where he is. " thanks guys, I'm honored to be been chosen for such an important role in such an ambitious war, and I'd hate to exploit your generosity....butcanikillalltheJewsandGypsiesandGaysandvariousotherpeople preeeeeeety pleeeeeeeeeeeaaaaaase?" "Why, it would be our pleasure! Go get'em bucko!" ...So yeah, Abstergo won't have any problem sacrificing a few Rent-A-Cops in one of their most crucial operations. Plus they may or may not even die, they just get whaled on with a baton.
 * While this would certainly be one hell of a Xanatos Gambit, it would also kinda be a dick move on Ubisoft's part, as there's no reason to believe Lucy and the other Assassins are anything but on Desmond's side. Lucy disarms two Templar guards, yes, but then she kind of...kills them, too (in an assassin-like manner too, if I recall). And while the Templars are certainly an organization that is willing to sacrifice its mooks, that seems like going a bit too far.
 * uh, dude? THE TEMPLARS WERE IN CHARGE OF EVERY SIGNIFICANT POWER IN WORLD WAR II AND PRESUMABLY ONLY DID IT FOR THE LULZ. *Ahem*, furthermore, it seems Hitler was like:
 * Kinda ruined by the fact that Lucy glows blue as an ally in Desmond's Eagle Vision.
 * But Al Mualim showed up as blue as well in the first game, meaning that Eagle Vision is most likely based on the perceptions of the user rather than being a 100% accurate representation of a person.

Desmond is the direct and perfect reincarnation of Altaïr and Ezio
He just learns what he, as the reincarnation of them, should know from his past lives. Note that Altaïr's and Ezio's names mean less or more 'Eagle' which is the symbol of the resurrection. Templars knew that and they abducted him to use him as they please by manipulating him into taking his past (but carefully cut/censored) knowledge. Also, he is the only one which can make proper use of Apple and Pieces of Eden, as seen with Ezio. Thus he's the The Messiah or The Chosen One and was hunted by Templars. But it took long researches to find him. That's why his parents sheltered his existence out of Templars' knowledge, because they were aware of his importance.
 * The eagle is the symbol of the resurrection? Huh?
 * Scroll to Eagle Symbolism and Legends: Ancient Cultures and here.
 * Oh, cool, I never knew that. Tv Tropes Will Enhance Your Life after all!

The Animus was based on the design of the POE-Apple
At some point, the Templars decided to try their hand at reverse-engineering a POE, the Animus was the result. An above WMG postulates that the Apples can send information forward or backwards through time. Two of the Glyph puzzles reveal that A) Humans were artificially engineered, and B) that humans have neural synapses that exist for no other purpose than to act as receptors, turning the POE's 'illusions' into direct stimuli. The Animus works by sending information from the past to the occupant as an 'illusion', the whole 'genetic memory' is just Abstergo Hand Waving the fact that they don't know exactly how it works.
 * Related to this is that Desmond's lineage is implied to be part Those Who Came Before. In one of Altaïr's codex pages, and confirmed in the ending, its revealed various 'gods' were the surviving TWCB, and Altaïr speculates that they had "real power, beyond these mere 'trinkets'". The bleeding effect is Desmond's Half Human Hybrid body learning to emulate the Apple's power on its own.

Each Animus requires a POE, likely Apple, to operate
Altaïr looked into the Apple one last time at the end of his life. Ezio may have done something similar. The Genetic Memory explanation is bullshit; Desmond can access their memories because the Apple keeps the minds of those who held it.
 * Except that when you're leaving the Absertgo Facility in ACII you.

The security system Desmond activated in the middle of AC II disabled Abstergo's guns and/or other equipment
And that's why a company with limitless resources came after their most valuable asset with batons.
 * Or they, y'know, wanted to take them alive.
 * Tasers? Tear Gas?... Beanbag launchers? There's a lot of ways to take down someone without it instantly being lethal.
 * Bonus theory! The Templar Mooks are all descended from the very few surviving guards of Altaïr's time, as all of them were Too Dumb to Live and total idiots. It could be the mentally deficient version of Eagle Vision.

Minerva didn't really know Desmond's name
Her speech was just encoded with an (INSERT DESCENDANT NAME HERE) command, and the Animus filled in the rest.
 * It's implied that Those Who Came Before had the ability to travel through time. If that's true, she really knew Desmond's name.
 * The novel Assassin's Creed: Renaissance likely confirms your theory

Abstergo ISN'T a Templar organization
It's an Assassin organization posing as a Templar organization. They've run at least 17 subjects through the Animus, trying to find as much as possible about the past Assassins (which doesn't really fit the Templars motives i.e. hide the truth and get their hands on the Pieces of Eden, why would they need the memories of past assassins when modern assassins would be far more useful for that?) and find someone who can survive the Animus AND gain the abilities of past assassins. It does also explain why the Abstergo logo appears at least twice in Minerva's speech at the end of ACII.
 * The Templars might want the Assassin memories because they don't know where the pieces of Eden are. Altaïr sees their locations at the end of Assassin's Creed I. Abstergo has been through sixteen (plus?) subjects because they keep failing to uncover Altaïr's memories, which would lead them directly to the Pieces of Eden. Also, Subject 16 wasn't finding pieces of Eden. He was finding the "truth," whatever that turns out to be. The Truth might also be a part of the Templars' nefarious plans.
 * You can also see the Abstergo logo on computer inside the Assassin's safehouse in the present. My assumption was that this was because the Animus 2.0 had been stolen from the Templars and heavily modified by Rebecca, Lucy, et al. The logos are just leftovers. Alternately, the modern-day Assassin symbol is the same as Abstergo's, in an attempt to sow confusion by one or the other.

Every single magical artifact from human legend and history was in fact real, and likely a Piece of Eden.
Admittedly, this is less likely to be a WMG and more a reasonable conclusion based on evidence given...

If AC3 takes place during World War II, the Assassin you play as will be the one who assassinates Hitler.
Subject 16 has already confirmed that an Assassin was responsible for taking out Hitler when he tried to escape his bunker. I don't think Ubisoft would pass up the opportunity to have you personally whacking him.
 * My theory is that if it takes place in World War II, you'll play as an Allie spy in an occupied France, while assassinating Templar Axis leaders.
 * Jossed for now. Also, even if it was set during World War II, it's unlikely you'd fight for the Allies,.
 * But not the Comintern thus if the setting is used you will probably play as someone from the Eastern Bloc.
 * Nonono, you'll assassinate Churchill. I don't care if he didn't die until '65 (it was an illusion cast by the Apple, or something), the chance to assassinate one of recent history's most beloved leaders is just too good to pass up.
 * Jossed. ACIII takes place in America during the Revolution. Still a possibility for future games, though.

Moses' staff and the Papal Staff are the same thing.
Due to the fact the game says all the miracles were done by pieces of Eden, and one of the pieces of Eden is a staff, and Moses used a staff, it shouldn't be too hard to piece together. So far we've only seen two Pieces of Eden, the Apple and the Staff. The Apple seems only good for making copies, illusions, or using the Jedi mind trick. The Staff is the one with real power. Also, Moses was the biggest prophet for Judaism, which later evolves into Christianity/Catholicism, which explains how the staff got to The Pope, it was just passed through the religions.
 * I'm pretty sure we've seen at least three pieces. If you do the Subject 16 puzzles, one of them is pretty much implied to be Excalibur and other famous swords.
 * The staff also briefly belonged to the Romanov Tsars of Russia.

The third game will take place almost entirely in modern day, with some parts following Altaïr's lover.
There's no reason for them to use the Animus, as far as I can guess. In the first game, they needed the map from Altaïr, and the second game was just training Desmond to become like Ezio. There's a point to all this training, you're going to fight as Desmond in the third game. This makes sense, considering the fact that Desmond now has a modernized retractable blade. Ubisoft also mentioned playing a female ancestor. Remember the flashback Desmond had when he was suffering the bleeding effect? Where his genetic memory is passed on to the Templar Altaïr had sex with? There has to be somewhere they were going with that, and considering that apparently Ubisoft says that you'll play as a woman, it's just too much to be coincidence.
 * We may get to play as a woman in her early stages of pregnancy too, who knows!
 * Jossed, it takes place during the Revolutionary War.

Petruccio had Eagle Vision
In the novel Assassin's Creed: Renaissance, Petruccio asks Ezio to bring him some feathers he saw on a high rooftop. After his brother does him favor he points out that he missed a few. It is impossible for a person with a normal sight to spot something small like feathers high on a roof so my presumption is that this kiddo might had Eagle Vision (being Altaïr's descendant and so).
 * Pretty solidly implied by the second game; Ezio's father tells him to use his special gift to find the secret door in the back of the family study, so it seems very likely that all of Giovanni's children have (well, HAD) Eagle Vision.
 * Expanding on this, Desmond's acquisition of Eagle Vision may not be completely the result of the Bleeding Effect; it could have just kick-started it. After all, Desmond escaped the Farm when he was sixteen -- it's entirely possible that he left before he was told about and subsequently taught to use Eagle Vision.

The Animus 2.0 simulation is experiencing Unreliable Narrator Syndrome via Desmond
This theory came from Australian Games Magazine Hyper (Issue 195 if you want to find it). The Review who did Assassin's Creed II pointed out this, that the bleed could go both ways, and that Desmond's memories and self were affecting things in the Animus, thus explaining the Shout Outs in the game.

Altaïr is One of Us
Obviously he played Super Mario Bros., see above.

Those Who Came Before are the Protheans.
Consider the nature of how the Pieces of Eden operate, and compare then with the technology of the Protheans. The Apple and the Beacons are very similar, and the effects of items like the Staff and the Sword are reminiscent of Mass Effect technology. Those Who Came Before also reported being destroyed by a calamity from the skies, which cuts awfully close to the idea of the Reaper invasion. And consider also that the Protheans were heavily interested in humanity.

Nathan Drake is related to Desmond
Distantly at least, which explains their similar voices. The Drake family branch broke away from the Assassins due to the betrayal of Sir Francis Drake becoming a Privateer helping the Templars in exchange for riches. When Sir Francis discovered El Dorado (A Piece of Eden bioweapon inside the corpse of One Who Came Before) he learned that his Templar benefactors planned to use it as a weapon for population control. He decided to redeem his family's honor by blowing up the Templar Island Base and hiding El Dorado. Gabriel Roman thought it was just a hidden treasure, but Navarro (who was a Templar agent) was looking for it, following the trail the Nazi's left only for destiny to intervene and return Nathan Drake to finish his ancestor's effort and redeem his family in the eyes of the assassins.
 * Later Nathan was pulled back into the war between the two factions by Chole (who is an Assassin) in order to keep Lazarevic (A Templar but not a popular one) from getting to Shambala which was an abandoned 'testing ground' for Those Who Came Before's genetic experiments on humans. Chole was supposed to consider taking Nathan, and the Drake family lineage, back into the fold but decided that keeping him out was better for him and better for the Assassins if they ever need a wild card.

If AC3 takes place during the 20th Century, the Assassin you play as will be the one who causes the Tunguska Event.
The turn of the century, turning Nikola to the cause, fighting Edison and J.P. Morgan's dark designs. It'll be The Five Fists of Science only without the Lovecraftian monsters...maybe.
 * Recently Jossed with the Assassin's Creed: The Fall comic series. Word of God states that the Russia-centered plot will eventually relate to the Tunguska Experiment.

In the end of Assassin's Creed 3 it turns out that the three games where played from the eyes of a descendant of Desmond who controls him the same way Desmond controls Altaïr and Ezio.
If the Third game is played from Desmond's point of view there wouldn't be any excuse why you could save, restart levels and do similar things or even look at Desmond from the third person perspective any more.

The logical conclusion is that in the far future someone wants to find an object which Desmond hides at the end of part 3. Therefore the Animus is used again. It would make the perfect meta WTF-ending.

Think about it. In the beginning of AC 1 development it was planned to keep Desmond's involvement secret until the end where all the animus-mechanics are revealed in order to make a good WTF-ending (it was thrown over due to information leaking).

Couldn't it be possible that they decide to pick this plan back up?
 * To make this even more WTFier than this theory is alone they should end the series with regular AC 3 with the release date in 2026 or later to imply that the player is indeed a relative of Desmond.

Word of God said that because it is Assassin's Creed 2, the protagonist has two hidden blades. That means in Assassin's Creed 3, the next protagonist will have three hidden blades.

 * I wonder where will he/she put the third one?
 * In his/her boot? Although that gives me some very bad ideas of how that blade is used...
 * The blade will be in the Assassin's teeth.
 * Isn't it obvious, bub?
 * On his elbow?
 * I don't hope Freud is right with his assumption.

The Animus is a time machine that uses Mental Time Travel instead of genetic memory.
Think about it. It explains the questionable aspects of 'Genetic Memory'. Desynchronization could just be a built-in failsafe against paradoxes. The bleeding effect would be due to his mind actually being there to absorb relevant information from his ancestors. It would also explain Minerva's knowledge of Desmond, as she is One Who Came Before and would therefore understand the Animus' time-travel properties.

You will have to fight Altaïr and possibly Ezio in AC3.
If you were enough of a dork interested enough like this troper to actually read the codex pages that you collect in AC2, you find a Cliff Hanger, where Altaïr is aware he is going to die soon, so he might/might-not-have used the Apple to save himself from death. He then might have been granted immortality or eternal youth only at the cost of being the Apple's slave for the rest of forever. Ezio might have become aware of his age himself, and used the Staff to keep him young forever, with the same rules to the contract that the Apple might have offered Altaïr. So when or if you play as Desmond, you will have to hunt down all the Pieces of Eden, and have to defeat the Keepers of Eden, people who fell under the control of the Pieces of Eden, possibly including Altaïr and Ezio.
 * If so, that will be a Player Punch of epic proportions.

The entire game takes place inside of a new, mass-produced version of the Animus, used for teaching purposes.
The Animus is the ultimate learning tool. What would be a better way to understand an event, than to actually experience it firsthand? That would explain why in the Desmond segments, the camera is still third person, and the entire series could be a simulation of how the Assassins defeated the Templars and helped mankind correct the mistakes it has made over the course of time.

Altaïr is the Father of Understanding
The theory goes that the oft-mentioned Father of Understanding is Altaïr after he used the Apple to live longer. To the Templars he would 'understand' their motives due to the side-effects and going revolutionize the Templars. The reason the Assassins weren't wiped out was because whoever he chose to succeed him - because he wouldn't have left them without a strong leader since he wasn't their enemy when he left to use the Apple - was too good and the Apple may have slightly decreased Altaïr's sharp thinking as part of the price of immortality. The new leader kept the information about what happened to Altaïr from the rest of the Assassins to prevent the obvious damage it would cause to their morale.
 * Maybe, but there is a historical father of understanding.

The Animus works by turning the inborn Psychometry skill up to 11.
Everyone we've known to use the Animus has had the alien Psychometric bloodline ability: Eagle Eye. The Animus just amplifies the inborn psychometry and tunes it up several notches, pointing it inward instead outward. If you were to put a "normal" human in the Animus, it would just be a hunk of junk.

Assassin's Creed takes place in the Tiberium universe.
The world is going to complete shit outside, and we never see anything beyond the facilities where the Animus units are being kept. The description of the chaos and destruction is very reminiscent of the collapse of national governments under the strain of Tiberium. Also, ancient societies and brotherhoods abound, along with Precursor technology. Clearly, someone is being manipulated by Kane.
 * Jossed: If you look out the windows in the warehouse it seems rather okay, also if you look at the signs in said warehouse you'll see they're written in Italian. Italy being the first country exposed to Tiberium.

Assassin's Creed takes place in the Dragon Age timeline
Assassins are Mages (I mean, how come they can do so many awesome things, unless they are Mages, specifically Arcane Warriors) and Templars are, amazingly enough, Templars. The Templars are in a role-reversal with the Chantry, since they control the religions. Quite obviously, Minerva and all those other things are the Maker, her minions, and all those Dragons. The Animus is just something that artificially induces the Harrowing through a Lyrium drip via IV.

Assassin's Creed III will be released on December 21, 2012
I can definitely see Ubisoft trying to pull this off.
 * Well, it's already been confirmed by Word of God that there will be no new Assassin's Creed releases in 2011...
 * They lied.

The multiplayer characters in Assassins Creed: Brotherhood will appear in the single-player story
The framing device for the multiplayer is that the player characters are Templars reliving their ancestors life's in order to gain their skills, like Desmond did with Ezio. As the multiplayer also takes place during the Renaissance, it is likely that these Templar ancestors where contemporary with Ezio, and therefore it is possible they may each have a role in the story. The most likely such role is as Templar operative's dispatched to kill Ezio. In particular, the Hunter class is likely to play the role of Ezio's Evil Counterpart, sporting a similar outfit (In the Hood worn with Badass Cape) and Weapon of Choice (the switch-blade, which promotional materials explain is a Templar equivalent to the hidden blade).
 * I can imagine the Courtesan being a Rival Turned Evil of the Rome equivalent to Paola and Theodora. She may even be connected to those two.
 * They did appear in the single player campaign. Ezio killed them all.

Every Assassin is spiritually bonded to the people destined to die by their blade/snake/spear/whatever.
This would be an explanation for the after-killing conversations Ezio and Altaïr have with their targets. They have a chance to talk before the bond is broken by the death and they go back to reality. In addition to that, they also can forgive their target and bring them back to life, which explains

There will be no Animus in AC3 and Desmond will learn to control the Bleeding Effect
As the Bleeding Effect kicks in, Desmond will start re-living the memories of his ancestors without the need to use an Animus, as he already briefly had with Altaïr in AC2. A significant part of the plot will revolve around trying to find a way to control the Bleeding Effect so that the visions don't just happen randomly. By the end, Desmond will have complete access to all his ancestors' memories (on paper anyway).

Assassin's Creed 3 will take place during the French Revolution.
Really, it's just so obvious choice. A conflict that fits perfectly in the series' theme, interesting period style, lots of beautiful historical buildings with plenty of decorations handy for climbing around...Can anyone give an example of another setting and period after the 16th century that has all that, and can convincingly tie to one mostly Caucasian man's family history?
 * Well, per The Truth puzzles, it is canon that Napoleon did mange to get his hands on a Piece of of Eden, which if I'm not mistaken is the same exact Piece of Eden that Altaïr and Ezio had for a bit (the Apple). So yep, it would be a perfect time period. They could set it from 1789 - 1815, which is the beginning of the French Revolution through to the Battle of Waterloo.
 * Adding in Napoleon would probably just needlessly complicate the plot. It would divide it into two parts that have almost nothing to do with each other. The Revolution itself has plenty to go for it, along with the fact that it had far more grassroot incidents that a single Assassin could credibly be a part of than the Napoleonian Wars. Plus that Maximilien Robespierre would be a far more interesting main villain; a man who goes from young idealist opposing the very institution of death penalty into a tyrant who executes dozens of people daily as counterrevolutionaries. That descent alone would make a magnificent central plot to the story, and the protagonist going from Robespierre's supporter into his worst enemy as the story progresses. Just for example. If Napoleon needs to be dealt with, a semi-sequel like the Brotherhood would be a better way to handle him.
 * Could be that Robespierre is a Templar Double Agent, used to infiltrate the Assassins. The whole 'get rid of the monarchy and install democracy' was in fact never going to happen according to Robespierre's plan. The Reign of Terror was what life was going to be like in the new Templar-controlled France. Permanently. That's not to say the monarchy was pro-Assassin. They could be, but they are probably neutral at this point. It could just as easily be that they were pro-Templar, and the whole Revolution was just a Xanatos Gambit to keep the Templars in control of France no matter what.
 * Like AC2, you could easily be fighting as another character like Ezio, perhaps a noble who was supposedly "lost to/erased from history." It would make it easier to get caught up with the crazy events that went on from the Revolution through Waterloo. And Napoleon wouldn't necessarily have to be an antagonist the entire time. Perhaps, in the chaos of the Revolution, the Assassins actually voluntarily GIVE Napoleon the POE, as he seems like the most reasonable person to wield it to bring France out if its Templar-orchestrated chaos (which one can historically argue that he was). Perhaps, they gave it to him just before 13 Vendémiaire (5 October 1795), which was the battle in which he distinguished himself and officially became a Badass. Maybe the POE causes Napoleon to lose it and become a megalomaniac. This forces the Assassins to turn against him, which they do by stealing the POE back during Waterloo, causing him to loose the battle and go into his final exile. However, the Assassin's don't kill him, as he may be useful in the future, though he dies before they can use him again.
 * "I know that symbol. That's a Phrygian Cap. It stands for freedom... and that, that's a Masonic Eye. Now those two come together in only one place--" Hey, what are those things on the Declaration of the rights of man and the citizen?
 * Close, but no cigar. It's finally been revealed that it is set in the American Revolution.

RED and/or BLU were part of/taken over by Templars.
In Brotherhood, one of the abilities your multiplayer character can have is the power to disguise yourself as someone else with amazing speed. Now doesn't that sound like an ability from a certain masked, suit-clad GENTLEMAN? Also, another ability, the Sprint Boost, gives a speed boost and swirly trail effects akin to BONK.

The Saboteur is the WWII Assassin's Creed
The Saboteur shares the building climbing of AC, has a car named Altaïr, and the trunk you need to steal from the Nazis could easily be a POE. It was outsourced to allow Ubisoft to create an AC in a different era, and keep it to a trilogy.

Assassin's Creed 3 will take place in World War One
The theory of a game in one of the World Wars has, after all, been passed around, and since World War II got jossed, perhaps it shall be World War One?
 * Possibly focussing on or including the Russian revolution, which takes place at around the same time.
 * Jossed. It does take place during a revolution, though: the American Revolution.

A closer-to-modern times AC will allow you to hijack a car while you're currently in another one and both are moving.
In Brotherhood Ezio can hijack someone else's horse while on one of his own. This is the (il)logical extension. Also, why the hell not?

Instead of horses AC 3: 2012 will employ motorbikes
Motorbikes are more a pendant to horses than cars and it fits that the first game suspicious specificly confirmed that Desmond has a motorbike license.
 * ASSASSINATIONS ON MOTORCYCLEEEEEES!!!

A closer-to-modern-but-not-quite times AC will replace horses with the bicycle

 * Now, that'd be just sad.

If the Prowler is voiced and appears in single player as a boss/target, he will be done by Barry Pepper.
The ultimate Actor Allusion/Take That: My hood-wearing guy is better than yours!
 * Jossed: The Prowler doesn't even appear in single player.

Lucrezia Borgia will be voiced by Brooke Shields
Considering that Brooke Shields is actually Lucrezia's descendant, it would make one helluva Casting Gag... Or whatever it would count as.

The entire series is in the mind of a conspiracy theorist tripping on LSD
It would explain everything.

Caterina Sforza is an Assassin.
Hey, it could happen. Did you not see her at Forli?! Perhaps in Brotherhood she may emerge as one. Funny, an Assassin with a foul tongue.
 * She's not technically in the Order, but she is a staunch ally of theirs.

Renaissance is canon, and is the true version of events
The protagonist of the novel is actually Ezio, rather than a simulation of him being controlled by Desmond. Wherever the novel deviates from the game, the novel shows what really happened, the game shows the Animus' imperfect re-enactment/Desmond behaving differently.

Ezio is Nanoha's ancestor.
As revealed in this trailer, about 1 minute in: "What are you going to do?" "Make some friends."

World War II was organized by the Templars to end racism and overpopulation
The Templars had wanted to get rid of prejudice for a long time (which is why they orchestrated the civil war), but despite all their success, prejudice was still alive and well in places like Germany and East Asia. To solve this, they orchestrated World War II and the holocaust. Everybody knows the affect this had on casual racists, they were disgusted by the actions of Hitler and the Emperor of Japan, and realized they were wrong (its more advanced than that in real life, but I'm not going to go into detail right now). After the war, enough support was built up to allow the civil rights movement to take place, as well as other equal rights movements in other nations. The war also served to set back overpopulation. This whole thing really fits into the Templar's whole Well Intentioned Extremist agenda.

Life is a giant Xanatos Gambit; don't believe a word anyone says!
So you've deduced that you're a Hashashin, and you want to find another. So you go and tell your BFF Forever (yes, Best Friends Forever Forever) that you support the Assassins, thinking "hey, they're my BFFF, they're just like me!" If you don't get a response of disbelief, sarcasm, or Idiot Ball, you might get the "oh hey, so am I!" Sweet! But...Templars never reveal themselves anyway, what with the Mind Control thing. So how do you know your BFFF is really an Assassin, and not a Templar in disguise? Or an Assassin disguised as a Templar disguised an Assassin?! Well, they're your best friend, so you can trust them with anything, right?

...right? Well you won't be believing that when you end up in an underground facility with your ex-BFF exchanging "I knew you knew I knew you weren't an Assassin!"

This goes along with the "nothing is true" part of the Creed; essentially, everything is a lie, doubt everything. Soon you (may) end up doubting your doubtings of your doubtings and end up just wanting everything over and done with. Or end up doubting further. Although I doubt that...

In conclusion: instead of opening your mouth, continue to pretend to be the Unwitting Pawn; the true Assassins/Templars (if you swing that way) will come to you.

Of course...who knows? All this advice could be coming from a Templar...

Sooner or later, we will be playing as Subject 16
They may as well have written "chekov's gun" in with their crazy scrawlings, and I cannot be the only one who's curious about them.

The Cain and Abel aspect of the story may be an inversion.
In the puzzle 'Brothers', Subject 16 notes that the Templars have always tried to put up there own people as the heroes (history is written by the victor after all). Also, in all three of the images of 'Cain killing Abel', Abel is reaching for the Piece of Eden as Cain strikes him down, almost as if Cain is trying to keep Abel from the Apple, just like the Assassin's have been doing to the Templars. And finally, an Assassin is a killer, just like Cain.

A later game will provide a Templar's point of view.
As it turns out, Maria is not the only Templar (or former one, at least) ancestor of Desmond. At some point in time, the Miles family tree happened to have a Black Sheep who became a Templar agent. While not a Complete Monster, said ancestor was something of a Anti Villain Well Intentioned Extremist who was likely just working for the wrong side. We now get to have a Sympathetic Viewpoint of the Templars as well as offer up some potential new gameplay elements.
 * As of Brotherhood, this is confirmed....sorta. The Templars are still bastards, but multiplayer is a training simulation at Abstergo.
 * For the purpose of clarification: A single-player campaign that has a Templar protagonist. That sounds kinda like DLC material though.

William, the Assassin sending intel to Shaun and Lucy, is Desmond's father
The M. at the end of his name stands for Miles.
 * Holy shit. Bill Miles was a character mentioned in the comic. So, this is very nearly correct.
 * This Troper agrees with this WMG. He also believes another WMG that is/was here that William was the male voice saying to put Desmond back in the Animus. This WMG is backed up by the fact that both William (or whom I'm assuming is William) and Desmond speak with the exact same accent, indicative of origins in Western New England.
 * I came across this today: Watch the video at this link (It's about the AC Encyclopedia): http://kotaku.com/5836272/assassins-creed-fans-and-game-writers-team-up-to-build-an-encyclopedia and pause it at 0:57 go to the characters column and read the first name under friends and allies. William M is William Miles. Confirmed, I guess?
 * Confirmed as of Assassin's Creed Revelations.  Barring the hints given by supplementary materials (the emails in the games and the comics), the fact that Bill was very protective over Desmond at the start of Revelations when Shaun implied that Desmond may have been "programmed" like Daniel Cross was was more than enough incentive to put two and two together.

Petruccio knew that Giovanni was an Assassin
The Assassins in Altaïr's time stained feathers with their targets blood. Maybe Petruccio knew this, and wants the eagle feathers to give to him. Also, it would have made for a good reason that he wanted the feathers.
 * Also a good reason to to have him executed, besides the reason given by Rodrigo at the end of AC II.
 * This brings up the question as to why Ezio was the only son who didn't know his father was an Assassin.

The Ones Who Came Before planned for the Pieces of Eden to be used to save humanity
But not by the Assassins. If you wanted something to get done long after you had gone, who would you trust to do it properly? The plucky, undertsaffed and out gunned guys with nifty fashion sense and some extra senses, or a global, powerhungry ruthless conspiracy with acces to the most modern technology of the time? I thought so. Every win the Assassins have had against the Templar plans have only weakened humaity's only hope. The OWCB don't care about our free will, only that their greatest invention survives in one form or another. Humanity is going to burn to death and it's all your fault, You Bastard.

When Desmond finally stars in his own AC game, it will be a Prince of Persia-style co-op game with Lucy as his sidekick
At the beginning of Brotherhood, there's a section with Desmond and Lucy This gameplay, with Desmond and Lucy helping each other get through, may very well be foreshadowing to when Desmond stars in his own game, which will be about him traversing the hidden Temples with Lucy a la Prince of Persia, with Lucy taking on the role of Farah/Elika/Whatever. Bonus points, because Nolan North has ALREADY starred as the Prince in the 2008 game.

Desmond isn't really in the Animus.
In fact, Desmond is long dead. His memories are being replayed by someone else entirely through an Animus.

The creators of the game intentionally left a glitch in the game after completing The Truth in Brotherhood
For those that didn't complete the truth until after the game there's a short scene out of the animus where the group discusses the ramifications. In it nearly everyone's version of Desmond was glitched standing through the Animus. This was intentionally meant for us to question and clue us into the fact that a glitch occurred in the "real world". The development team has been noted for blaming all glitches and bugs in the games on the Animus, why would they leave such a common bug unless it was meant as a plot point?
 * I think they've patched it. Video Game Tropes do apply outside the Animus now too. There was a loading screen.

Subject 16 lives yet.
Who here has taken the Assassin's Creed: Brotherhood achievement for completing all the glyphs to a morse code translator? I'll tell you.
 * I figured he managed to

The announcer for Brotherhood multiplayer is an AU version of GLaDOS.
Not much real evidence other than sounding vaguely similar, but it sounds cool?
 * She's the same Animus voice that appears in the first game...
 * Still applicable.

Desmond had to kill Lucy so he could have a child with someone else.
Combine the ending of Brotherhood with Subject Sixteen's 'The Truth' and you realize that Desmond is not the important one. His son, who is of Templar descent, is using an improved nearly-glitch-free animus sometime After the End. Desmond was falling in love with Lucy and she had to be eliminated so he could find the one.

The Patriots are tools of the Templars.
The way the Patriots control the public opinion and media would be just in accordance to the Templars' goal. Big Boss and later Snake and Raiden became Assassins to oppose them.

The explanation of Synchronization
It's not about how close to the original memories the gameplay is, it's about how well Desmond understands his ancestors. The reason the sync bar goes down is because he doesn't understand what it's like to have a sword slice you, and yet still be able to walk away from it as Altaïr and Ezio do, or drop off a building and walk away. The reason it increases in the game is because Desmond started to understand his ancestors better and better - he starts off seeing Altaïr as proud and strong, something Desmond probably can relate to in some capacity, but then saw the guy stripped of all his possessions and rank, which he can't understand at all, and he sees Ezio start off as a rich and happy noble, which he could never imagine. But over time, he saw the sights they saw, he got into their minds and bodies, and learned about them more and more, just as Altaïr and Ezio understand themselves more in their own journey, thus increasing the synchronization more and more.

The Sisterhood Cheat is Actually Canon!
And Ezio ended up sleeping with each female member of the Assassin's order he founded, eventually resulting in multiple Ezio/Altaïr descendant lines!

Lucy is Erudito
She knows the ins and outs of Abstergo, and she's probably in charge of the gang's email network, so she likely would have the passwords to give to Desmond.

After Ezio discarded his father's Assassin robe, The Smuggler found it.
It's sort-of similar in appearance to the robe she wears in Multiplayer (note the neckline, puffy white sleeves and leather cuirass), and her scenes in Project Legacy make her seem like the type of person who wouldn't mind wearing a dirty, 40 year old robe.

Cesare Borgia will be resurrected at some point.
A new Mmemonic set in Project Legacy is based around The Shroud. The components are Jesus, Brutus (briefly rezzed in another memory), some other guy and Cesare. Factor in Ezio's uncertainty over his last words, and his unwillingness to die in the final boss fight and Ubisoft may as well have outright confirmed this! Unless they're playing with us.
 * Actually, the other two components, alongside Cesare and Jesus, are Jacques de Molay and Geoffroi de Charny, but here's the thing: Jacques de Molay was the last Grand Master of the Knights Templar, or rather last known Grand Master in the Assassin's Creed universe, and Geoffroi de Charny and his wife are the first recorded owners of the Shroud. Also, as the last Grant Master, there were many legends surrounding Jacques de Molay including a connection to the Shroud.

Lucy is a Templar spy.
She got Animus data to Rebecca while at Abstergo, can get into Abstergo's mainframes easily enough after leaving, encountered very little resistance while escaping, and later in the game, if you talk to Lucy and then go outside, she is standing right where the red footprints leading to the vila end.

The Apple can store consciousness
We already know that Altaïr looked into the Apple to see about preserving his mind as he approached death... but it could be possible that the Apple itself would serve as the vessel. In Brotherhood, Ezio becomes a lot more cold and controlled. He's still a bit of a Lad, as he always was, but he comes off as being a lot more calm and calculating, and a lot less concerned with having his fun and charging into a fight. This could be down to his age, his weariness at the neverending war against the Templars or the wisdom he gained over the years, but this change in him comes about right after he first uses the Apple against Rodrigo Borgia. It could be that upon using the Apple, Altaïr's mind entered Ezio's body, either taking over him completely or merging itself with his without his knowledge. This would have brought about the change we see in Ezio - either he absorbed Altaïr's mind or got taken over completely. If the former is true, then Ezio could have adopted many of Altaïr's personality traits, resulting in his quieter, more patient temprament. If the latter is true, then Altaïr may have retained Ezio's memories or experienced a similar effect on his personality. With Ezio's memories he could convincingly pass it off as if nothing had changed, and his warmer, more personable character could have been either from maintaining his cover or from picking up Ezio's traits. It may also be possible that a combination of the two men now exists within Ezio's body, perfectly aware of what has happened. Whatever the case, it may have been that Ezio placed the Apple within the vault beneath the Colloseum and left the writing on the wall of the sanctuary passage in order to ensure that Desmond could find it. While he could have placed it there simply to ensure that it could be used to prevent the end of the world (Ezio could have consulted the Apple to see what lay ahead, and learned about the coming apocalypse regardless of any alterations to his mind), it could also be possible that he wanted the next bearer of the Apple to experience the same effect, in the hopes that the wisdom and knowledge of both himself and Altaïr, both held within it, would be passed on to the next person who would really need it. If this is the case, then Desmond will be a very different person when we next see him in a future installment.

Juno forcing Desmond .
(Theory courtesy of the Ubisoft forums) The more you think about the popular theory that Juno because Lucy, the less it makes sense. Lucy went through a hell of a lot of trouble to defect to the Assassins, defying Vidic and all the other Templar higher-ups, and even if we're assuming she managed to, that's an awfully roundabout way for Abstergo to get the info they need, considering Desmond would have never escaped the Templars' clutches without Lucy's help.

So, essentially, Lucy would have had to assuming they wouldn't just kill her for her efforts. Either that or this was all a convoluted Templar plot to, but why would they even need that if they have Desmond right where they want him? So which is more likely? That Lucy by Juno for her efforts, or

It was all a trick- As if that wasn't enough, in the very first game we're shown that the number one power of the Apple of Eden is  Next time you watch the AC:B ending, pay close attention to what Juno says.

The next game will have Desmond on his own, using the Apple of Eden as a portable Animus.
Pretty sure killing Lucy wont go over well with the rest of the team even if Desmond explains that he was being controlled. Either they kick him out or Desmond leaves voluntarily in case this happens again. When Desmond sleeps the apple will automatically shape his dreams to reflect the memories of another past life, someone different but relevent to whats going on in the present.
 * That's improbable. The team needs Desmond, regardless of whether they like him or not. On the contrary, if Desmond tried to leave, they'd do their best to stop him, what with the end of the world coming and all if they don't do something to stop it. He might be treated more as a captive though. It's unlikely that they would treat him as a traitor though; they know the Apple's powers well enough, but that wouldn't stop them from considering him dangerous under its influence.

The Hidden Blade is a Nasuverse-style conceptual weapon.
As long as its user takes the enemy by surprise or counters the enemy's attack successfully, it will One Hit Kill no matter what. Like the Mystic Eyes of Death Perception, though, the question is executing the move. Good enough against the games' human opponents, but against the Eldritch Abominations of Nasu's setting...?

(Warning: Spoilers for The Fall) That old guy in the white suit wasn't the Mentor.
If you want to bring someone to meet you, the only rational reason to kidnap them instead of, you know, sending an invitation is because you don't trust them. And if you don't trust someone, why on earth would you leave them alone in a room with the head of your entire organisation and a deadly weapon?

The Assassins aren't that stupid. They set up a convincing-looking stand-in for the Mentor in order to draw out possible traitors. The REAL Mentor is alive and well.
 * The Mentor seems to want to hold certain mystique about his existence - hence the kidnapping. But according to his words, the Mentor isn't so much an individual than a collection of memories and thoughts of dozens or hundreds of people throughout ages. They can't have gone so long time with just one guy passing a torch to another - they must have the means to create a new Mentor, perhaps out of anyone with a genetic link to the original Assassin heritage. But the reason why the Assassins are in so great dissarray in the games is that Daniel told the Templars about all their major compounds, so it can't have been entirely planned out affair.

The Ones Who Came Before are the Great Race, HP Lovecraft's Yithians.
Pre-human civilisation? Check. Technology so advanced it looks like magic? Check. Mind-altering powers? Check. Underground stasis vaults scattered across the world? Check. Time travel or precognition abilities? Check. Strong but dispassionate interest in humanity? Check.

This ties pretty well into the previously-mentioned WMG that the Animus uses mental time-travel rather than genetic memory, too. Mental time-travel is what the Yithians were famed for.

Assassin's Creed III will take place in New York.
The coordinates Ezio and Leonardo get at the end of the Da Vinci Disappearance DLC point to an address in New York. Perhaps the two guys who took Desmond back to the Animus are leaving to New York as their new hideout, or one of Desmond's ancestors lived in Upstate New York?

The Pieces of Eden can also function as Energon Harvesters.
They have to get their energy from somewhere. So they are built with a means to extract energy/energon from any source to power themselves. Optimus Prime referred to the one in his show (looked like an Autobot scaled Apple) as being built by the ancients, but he's referring to the Ones Who Came Before and not ancient Autobots.

La Volpe is related to Ezio.
It was implied in Assassin's Creed II that La Volpe has Eagle Vision (thats how he sees through walls) and it has been stated that only descendants of Adam and Eve (like Altaïr and Ezio) have Eagle Vision, so La Volpe must be descended from them, therefore related to Ezio.
 * There must be dozens if not hundreds of family lines originating from the first Assassins. La Volpe doesn't need to be a close relative; he could be a distant cousin of nth degree, from crossing family lines a millennia back.

Eagle vision allows the user to see all around them.
Think like Wrath's Ultimate Eye - it allows them to see 360 degrees all around them, at all angles. Thus, the camera isn't just an animus thing - it's Altaïr's and Ezio's actual vision!

The Assassins are trying to train Desmond to be the next Grandmaster of their order.
After The Fall, and the Assassins need a new leader. If they already have one, they're probably just an acting leader, ala Machiavelli after Mario was killed. After all, both of Desmond's ancestors played as so far were Grandmasters in their perspective generations, and Desmond even commanded a few Assassins through Ezio in Brotherhood.

Daniel Cross (from The Fall) will be a rival and maybe even antagonist to Desmond.
He's got a lot of Assassin skills, and he's

Desmond is from...where? "The Farm" is in...
C'mon, let's hear some guesses!
 * Western New England. Mostly cos I think that'd be awesome, but also because Desmond speaks with an accent indicative of someone of middle class background from west of Boston. And also cause his voice actor is from Connecticut.
 * New Mexico (Desmond mentions it being in a desert IIRC and NM is the most desert-y place in the US this non-American troper can think of.)
 * American troper here, the southwestern United States has quite a bit of desert, extending from the western parts of Texas, through Arizona and New Mexico, southern California, Nevada and Utah.
 * According to the Desmond's Journey sidegame in Revelations and the Encyclopedia, The Farm is in the Black Hills in South Dakota.

The final Assassin's Creed game will focus on Desmond's mother
I originally thought that the final AC game would center on Desmond, but there's a problem - namely, how central the Animus is to the gameplay. For Desmond to be the sole protagonist would require significant changes in gameplay. Instead, we will have a parallel plot of Desmond and his mother (who we will call "Mom" for now). The Mom storyline will take place in the Cold War, and could span the globe. Desmond will get plenty of screentime, and players will control him using a slightly different scheme.
 * This was altered from my original theory. With Desmond's father now a major character, there would be little reason for Desmond to explore his dad's memories. If his mom is dead or missing, on the other hand, then there could be plenty of reason. Especially if, as other WM Gs have suggested, his mother is the one with the stronger bloodline.

Rosa is Desmond's ancestor
While Ezio had many love interests, most of them were nobles, for whom an out-of-wedlock pregnancy would have been devastating. By contrast, Rosa is a commoner, and an out-of-wedlock pregnancy would not have harmed her social status.
 * Plenty of noblewomen had children out of wedlock, as they had the resources to keep it under covers. But in any case, it's still possible for Ezio to marry after the events of the games.
 * Jossed: Although there's still a possibility that Ezio and Rosa had a kid on the side we never saw.

Memories can only be passed down the male line.
Because of the way biology works. Men create sperm all their lives, and according to the way that genetic memory probably works, DNA memories are updated in every batch of sperm. Meanwhile, women are born with their entire supply of eggs already formed.
 * But both kinds of gametes are still formed from germ cells which are segregated from somatic cells very early on in development. Genes in somatic cells are modified throughout life according to the particular cell type's needs, but germ cell genes are not.
 * Anyway, Jossed by the multiplayer which is part of the canon: you can see several women among the Animus-users in the opening, and there are several female character options to choose from.

Assassin's Creed is a Deconstruction of Stealth Videogames (Or, just games in general) SPOILERS for the ending of Brotherhood
Not sure if this has been talked about yet, but I got the idea after finishing Brotherhood. At the end,the Apple of Eden and the Desmond sequence fully drives home the idea that this is a deconstruction of video games. First, with the Apple of Eden, Ezio is virtually unstoppable, and getting the badies out of the way is done by holding down or pressing one button. In terms of gameplay, you are as close to God Mode in Assassin's Creed as we're likely to get. One must remember that the player isn't the only one "playing;" Desmond is in the Animus, and is "playing" the memories. We control Desmond, and Desmond controls Ezio.

Later, after we finish the parts in the Animus, we play as Desmond and have to go get the Apple under the coliseum. The pause menu is very different; the only options we get are Resume, Options, etc. Regular game options. Whats missing is the ability to restart: this is important because without that ability, it means this is the real world, and we are Desmond in the here and the now. We are no longer "playing a game;" there are no retries or redos. It is also impossible to die (I believe; I fell a couple times jumping around the church and didn't die when I presumably should have) probably because, if Desmond did die here, he would be dead forever. The developers didn't want to turn the players into a bunch of suckers if they did fall far enough, but also wanted to stay consistent. They couldn't let Desmond die here.

When Juno takes over Desmond's body and murders Lucy, we feel what its like to be controlled. We make the movements, despite not wanting to, and we're entirely conscious of it. We hate killing Lucy. We are being "played" by the equivalent of God. This is the same feeling a video game character might feel if, say, you played a cruel mother and killed random civies, if they were conscious of it. Also, the ending, being put back into the Animus (the game) because its the only way to save Desmond is similar to falling into video games because of grief, that might stem from, maybe, being forced into killing a friend of yours.

I'm sure there are other examples throughout the series, but these are the ones that stood out to me the most.

Cain is still alive.
And in the final Assassin's Creed game, Desmond will kill him.

The Freemasons are Assassins.
Compare their symbols. They look rather similar, if you ask me. Besides, it would be a twist for such a maligned organization to be on the good guys' side.
 * The AC wiki says they're Templars, though the evidence suggesting this is circumstantial. I am currently debating this issue here, here and here. (NOTE: This has since been fixed.)
 * It may not be confirmed outright, but there's lots of evidence to support it. George Washington and Teddy Roosevelt, two US Presidents who were Freemasons, were confirmed to have had an Apple, and one of 16's notes indicate that it was the Freemasons who brought it across the pond, so it's certainly not a coincidence. The Freemasons were always extremely secretive, and some real-life conspiracy theories claim the Freemasons are Templars who control the US behind the scenes (lots of the conspiracy stuff in AC is based on real theories). One theory also blames the Freemasons for faking the moon landing, which was confirmed to be not fake but a Templar mission to get an Apple that was on the Moon for some reason. Too many coincidences for me.
 * The Freemason ideals have many things in common with both the Assassin and Templar ideals. It's possible that both sides are infiltrated in their ranks and trying to control the organization for their own ends.
 * Confirmed most of the Freemasons end up being the friends of Connor the protagonist of AC III including of course George Washington. So yay you don't have to kill him.

Ezio may have met with RKS Members.
They're in the same era.

The series is in a Stable Time Loop, and Desmond and Adam are the same person.
This would explain the the "precognition" of "Those Who Came Before". This would also explain why Desmond and Adam are voiced by the same guy.

Marquis de Sade will feature prominently in AC 3.
Assuming that the earlier WMG about AC 3 being set during the French Revolution is correct, de Sade would most likely to be a prominent Assassin of the period. Much like Machiavelli, de Sade is a historically vilified figure associated with all kinds of unpleasant activities, but who actually was ahead of his time in many ways, defending women's rights and opposing class society despite of his aristocratic station, like Machiavelli supported the idea of republicanism in most of his less known works. And to tip of it all off, certain writings of his almost directly state: "Nothing is real, everything is permitted"!
 * Possibly. It's confirmed that it takes place during the American Revolution, but the time period still definitely fits. The core ACIII game seems to be based around America, but exploring events in France and the rest of Western Europe is definitely a possibility for spin-offs. This being the American Revolution, it's likely that the Marquis de Lafayette will put in an appearance at some point, so his entry into the saga would be a nice bridge between events in America and France. If we do get to France in a future game, I doubt the developers would pass up a chance to work Marquis de Sade in somehow. (I actually have a similar WMG about this on the page for Assassin's Creed III).

AC III will take place during The American Civil War.
It's arleady established that John Wilkes Booth was killed by the Assassins, and that Subject 16 had an ancestor at the Battle of Gettysburg (who may or may not be a common ancestor between 16 and Desmond). The Battle of Gettysburg is also perfect for nicknaming this Assassin "The Killer Angel".
 * Jossed. It takes place during the American Revolution. Close guess, though.

Jupiter is the the one who seeded the Assassin line.
Considering how the mythological Zeus/Jupiter liked to mess around with mortal women, that his wife Hera/Juno was known to be a bitch towards said mortal women (and their offspring -- think Heracles/Hercules and his reason for starting the Twelve Labors), and how one of his motifs was the eagle, and it makes a lot of sense.

Altaïr's storyline in Assassin's Creed Revelations will be used to justify Bag of Spilling.
The game will begin with Ezio having all his equipment and skills from Brotherhood intact. When we eventually control Altaïr, he will start off with only the weapons he had on him at the end of the first game (or Bloodlines, but I haven't played it). Over time, he will slowly gain the weapons and skills that Ezio currently has, possibly showing the events that lead to him looking into the Apple of Eden and developing the Hidden Gun, the current version of the Hidden Blade, and other weapons. We will eventually switch back to Ezio some time after Altaïr gains all of Ezio's current skills and weapons in his storyline.
 * Jossed according to the information currently released. The game will mainly follow Ezio, but will be able to take a look at Altaïr's life through special seals.

In Revelations, we will play as Altaïr's son, not Altaïr himself.
Desmond has already witnessed the said son's conception in Assassin's Creed II.
 * Related: Altaïr's son will also be named Altaïr so we will be playing as "Altaïr", just not the one we're familiar with.
 * Possibly jossed. As mentioned above, special seals will allow Ezio to peer into Altaïr's life.

The Assassin's Creed games were marketed by the Assassins themselves.
Think plot of The Last Starfighter. The Assassins in fact control Ubisoft in real life, and are using the games of the AC franchise to get the word out there about their war about the Templars and their secret war. The final game in the franchise will be specially tailored to each state/province/etc. where it's distributed, with contact information for local Assassin cells to contact as a hidden easter egg. Only the most serious and talented gamers will be able to access this easter egg, and thereby be recruited into the order.

The Assassin's Creed games were marketed by the Templars
Think about it. They were only a few years from launching their satellite when the first game came out. The Assassins may become desperate and try and appeal to the public to help stop them. But to prevent this, the Templars either infiltrated Ubisoft or convinced the company to make the games. This way, if any of the Assassins or Assassin sympathizers try to inform the public of what the Templars are doing, they will only be marked as "insane and obviously plays too much video games".

Cesare Borgia really isn't able to be killed by a mere human.
And he probably will come back in Revelations and turn out to be the grand master of the templars. Alternatively he still lives in 2012 and is Vidic or some other higher-up of Abstergo.

A future game will allow Desmond to die.
But instead of respawning, the game will just cut to a silent black screen with nothing on it. The only way to retry the level will be to quit the game and restart it.

Desmond's game will take place After the End.
The solar flare destroys most of the world's power supplies, so Desmond is forced to crawl out of the animus (it hugely malfunctioning as the Assassins try desperately to log Desmond out before it fries his brain could make for a trippy tutorial). The almost complete destruction of society would be a great excuse for the small city sizes, the lack of population and the lack of supplies of the guards/military. The plot could have Desmond tracking down the temples, to ensure nothing like 2012 happens again, or finding a viable method of Time Travel to get back in time and stop the flare before it does any damage.

Eagle vision is actually a mild form of Omniscience
The precursors' sixth sense, "knowledge" is omniscience. Minerva knew that Ezio would find the vault under the Vatican, and how Desmond would eventually see the message via the animus. Juno also mentions that the humans "see the blue glow". Just like how Eagle Vision makes various people glow. It also explains how Ezio/Altaïr can use their eagle vision to identify people they've never met before, as well as things like guard patrols and secret, invisible messages that should be imperceptible. Ultimately, the gods used their future knowledge to leave relics and messages to ensure humanity's continued existence.
 * Whoa. I had a theory almost exactly like this. To elaborate on yours a bit, Eagle Vision appears as vision because it's the only way for humans to perceive it; their brains simply can't interpret the signals they're receiving any other way. If our brains were more developed, we could sense the knowledge in a different way, one that we currently have no baseline for.

The Sicarii were the ancient Jewish precursor of the Assassin Order
Just read that article! Concealed daggers, anti-Roman zealotry, you name it. The Sicarii were basically the Hashhashin, before their time. Bonus points because they would blend in with the crowd by pretending to mourn their victims.

Assassin's Creed III will take place in the Thirteen Colonies during the time of the French and Indian Wars and The American Revolution.
It makes sense. A resource-rich territory is a perfect battleground between Assassins and Templars. If George Washington doesn't turn out to be a Templar, he's a perfect Assassin Grand Master, as historians already believe him to be one of the great military spymasters of the era. Hell, the Founding Fathers might even not be aware that some of their fellow leaders are Assassins or Templars, which could lead to a fundamental split in ideology between them (one that can be seen later in the Federalist (Adams, Hamilton) and Democratic Republican (Jefferson, Madison) divide after the Revolution. They could use colonial cities like Boston, New York, Philadelphia, Baltimore, and Charleston as settings. Granted, this is likely more possible if the majority of the Patriots were Assassin-aligned, and I have a sneaking suspicion Thomas Jefferson would have been the preeminent Assassin anyway, while Benjamin Franklin served as more of a da Vinci role.

Besides, the AMVs using songs from Seventeen Seventy Six would make it all worth it.
 * While the ideological setting is near-perfect, the United States of the period lacks the distinctive architecture so prominent in the games so far; adventuring in 18th century American cities would be rather dull compared to Chrusades era Middle-East or Renaissance Italy. Also, the locations used so far have been picked on the basis that they appear exotic, but average gamers can still recognise landmarks and individuals here and there. Setting the third game in the US would make the events too familiar to the American gamers, as well as stretch the suspense of disbelief farther due to the more familiar history.
 * Confirmed! 'Assassin's Creed III will take place in the French and Indian Wars to American Revolution period.

Desmond's bloodline has a thing for Second Loves.

 * Altaïr had Adha, but she was kidnapped and killed, and in the Codex in AC II he admits that he loved her. Instead, he ended up with Maria, a Templar turncoat.
 * Ezio had Cristina, but she refused to come with him and From the Repressed Memories in Brotherhood, it's pretty clear he loved her, and if his other relationships are anything to go by, he hasn't had anything similar since. Revelations will most likely feature Ezio's Second Love, and probably bring an end to his storyline via the conception of Desmond's ancestor.
 * Well, Ezio does meet his second love Sofia, but his children aren't conceived in the game.
 * Desmond has Lucy, but Juno tells you "there is another." The meaning is pretty obvious. Which leads to...

Assassin's Creed III will be set during the French Revolution.
At the end of Brotherhood, while in the Vault, Shaun mentions the Phrygian Cap, which stands for freedom, and the Masonic Eye, and says they only come together in one place before getting cut off. That place is the Declaration of the Rights of Man at the beginning of the French Revolution; the cap is on the tip of the spear, and the eye is in the middle in the top. Like the Crusades and Renaissance, most people know about the French Revolution, and would recognize some people, but be in the dark enough to not know everything. Like II, it could span multiple years, possibly going into the reign of Napoleon. Incidentally, the Glyph puzzles in II mention that Napoleon possessed a Piece of Eden; this would give the Assassins and Templars a reason to go after him.

Desmond is Subject Sixteen.
"Desmond Miles" is a false personality generated by Sixteen to cope with the Bleeding Effect.
 * Jossed in Revelations.

Spanish civil war will be in 3.
it seems logical, it has a chaotic good vs lawful evil/lawful neutral just like the rest of the series

AC 3 will centre around the first descendant of Altaïr and Ezio.
According to the writer of Revelations, Altaïr and Ezio are on different sides of Desmond's family tree... which means that at some point, the descendants of Altaïr and Ezio intermarried. Since when that happened hasn't been revealed, AC 3 can take place any time from 1530 or so to the modern day (Desmond might be that first descendant).
 * Desmond is the convergence of Altaïr and Ezio's bloodlines. Also, Sofia being a descendant of Altaïr is a very big stretch since until meeting Ezio she wasn't involved in the whole Assassins Vs. Templar business.

Locations of Minerva's Temples.
Let's hear some guesses!
 * Rome, New York, for obvious reasons having to do with the Da Vinci Disappearance.
 * Mystery Hill, Salem, New Hampshire, because it is an inexplicably old archaeological site not matching anything that the native groups built in the area at the ethnographic present. That site, and others like it around New England, while obviously man-made, have the native tribes of New England just as perplexed as the archaeologists.

Subject 16 is...

 * Cole McGrath.
 * James Heller.
 * Nathan Drake.
 * Batman
 * going to try and pull Grand Theft Me once Desmond unscrambles his memories.
 * All of the above?
 * None of the above, actually.

Rosa is Vin
"Jump implausibly high and scale tall buildings
 * Okay, firstly the physical resemblance is pretty strong, both thin, short girls with black hair and a preference for male clothing. Secondly, they can both:

Move incredibly fast on the ground

Do so while having sustained what would normally be fatal injuries

Survive said injuries and make a full recovery with only primitive medical aid

Knock over large men in metal armor with a physical shove

Knock over large men in metal armor from a nearby rooftop"


 * Their personalities might not be the same, but Vin is not exactly incapable of playing a role.

Assassin's Creed III will not feature Desmond at all.

 * Bear with me. In Brotherhood, Juno and Sixteen talk about a woman that will help Desmond defeat the Templars and save the world. Specifically, Juno says that it is not Lucy, and that Those Who Came Before cannot sense her ("the Cross clouds the horizon"), thanks to the Templars. Sixteen, meanwhile says that the key is Desmond's son. Then in Assassin's Creed: Embers, we met a female Chinese Assassin named Shao Jun. The order has been annihilated by the new Emperor and she travels to Italy to seek help from a retired Ezio. After a short period where Ezio refuses, he offers her advice and a parting gift (to only be opens when she loses her way) before she returns to China. This is such an enormous plot hook that it can't possibly be not followed up. Put it together: AC III will follow Desmond's female counterpart, either a Templar or an Assassin/regular person that Abstergo is using to explore Shao Jun's memories in their continuing quest for world domination, who will ultimately escape (or be set loose) and track Desmond down.
 * Or it'll star Daniel from The Fall.

Shao Jun will be the ancestor character in Assassins Creed III
If only because Embers showed her to have a hidden blade-type device in her shoe. With one on each wrist...
 * That would somehow require her to be related to either Altaïr or Ezio. Also the next game will likely move beyond The Renaissance.
 * Technically, she only has to be related to Desmond, and later Ming Dynasty China is pretty different from Renaissance Italy...

More on Lucy as a Templar spy...
She is one, but not in the way most people would think. When this troper played through Revelations, specifically the part where Shaun suggested to Bill that Desmond may have been programmed by the Templars, it got the troper thinking. Perhaps Lucy was somehow programmed at some point in her life just after she became an Assassin (most likely during her undercover stint as an Abstergo employee in the first game). That could be what Juno meant when she said "the Cross darkens the horizon" regarding Lucy.

Desmond will relive the life of a Templar ancestor.
Think about it. What better way would the Assassins have to gain intelligence on the methods and motives of the Templars? Relive the life of a Templar. There is already a high chance that he has at least a few Templar ancestors. Maria, a former Templar, is already one of Desmond's ancestors. It wouldn't be to outlandish to think that she was born into the order from her side of the family. Therefore, they would also be Desmond's ancestors, allowing him to experience their lives through the Animus. Obviously, this would be a bit of a radical change for a main series game, but it would make a nice side-addition.
 * Her entry in the in-game Database and Encyclopedia seems to suggest she wasn't. Then again, there's nothing that explicitly confirms it...

If there's ever a modern-day game, will be The Dragon to Alan Rikkin.
After all, he  and the multiplayer mode of Revelations confirms he's both still alive in Desmond's time

The neurotransmitter that PO Es use to enslave humans is the "genetic pump" described by Warren Ellis in Supergod
Morrigan Lugus describes faith as a narcotic effect "triggered by awe and fear of an anthropomorphism of your environment." In prehistoric times that translates to "sky gods" in the clouds and rolling hills mistaken for "earth mothers", but in history this role is mostly played by smooth-talking demagogues. If you are suspicious of authority, due to knowing "nothing is true"(anyone who claims to have all the answers is so full of shit his eyes should be brown), and "everything is permitted"(no two societies have the same laws, so they are made by imperfect people and you should use your own judgement of right and wrong) you can call the pig out and demand straight answers which he can't provide. If someone with strong will and that same suspicion is hit by a POE, they can realize the effect is an override and choose to resist it.
 * Fun theory: if this is true, then it may be possible to create some kind of biological countermeasure - a drug or a genetic treatment that makes you immune to demagoguery as well as PO Es. That would be a revolution equivalent to the invention of writing.

Subject 16 has relived Shao Jun's memories
Lucy mentions he lived the life of an ancestor in the Far East, and if you read the blood wall above Desmond's bed, there are multiple Chinese sentences and even an explicit reference to Emperor Jiajing.

The Crystal Skulls will be vital to Assassin's Creed III
E-mails Desmond can find at the end of the first game make mention of them (along with other unimportant plot aspects like Subject 16 and the Bleeding Effect), specifically that the Templars hold them in the modern day and use them as untraceable communicators, and that Vidic himself is in possession of one. Meanwhile, one of the few English phrases on Subject 16's mural reads "Within Quetzalcoatl's hunger and Emperor Jiajing's sin lies the answers". In Project Legacy, we see Giovanni Borgia steal a Skull from an Aztec city, and he is later contacted through it by a Chinese man, who is most probably Jiajing. Given that the skulls from Mexico and China are probably what 16 was referring to, maybe the "answers" he says they contain are the solutions to the solar flare Jupiter mentions he, Juno and Minerva were working on at the time, that Desmond and co. will have to find, by digging through Shao Jun's memories to find the Jiajing skull, and preparing an assault on a Templar facility convieniently located in New York to get Vidic's crystal skull, giving Desmond a chance to finally get some revenge on Dr. Vidic.

Erudito is Consus
In the final entry of Divine Science: Chapter 1, it is revealed that Giovanni Borgia gets possessed by a member of Those Who Came Before, self-addressing as "Consus, the Erudite God." Erudite as in "Erudito", perhaps? It's known that Those That Came Before are both long-lived and anti-Templar, so it wouldn't be surprising if such an entity decided to meddle in Abstergo's affairs.

Assassin's Creed shares a timeline and world with Grand Theft Auto
Or possibly Saints Row.

La Volpe is Hermes
We already have a cast of Greek Gods, and one of the things Hermes was the god of was thieves. The Hermeticists wear outfits similar to his. And this would explain why in the thirty-some years years of AC 2 and Brotherhood he appears to not age and even get younger.

Assassin's Creed III's plot
In light of the newly released images of the game, establishing an American Revolution setting and a Native Assassin, Tthis troper decided to do a bit of reading up on the American Revolution on the Other Wiki and searched up the roles the Natives played in the Revolution. To her surprise, most of the Native Americans sided with the Crown, and one of the powerful supporters was Joseph Brant of the Mohawk nation. Said nation was a part of the Iroquois Confederacy based in New York. A possibility that our Assassin will see the events of the Revolution unfold from here, who knows? It would make sense considering the key to saving the universe is in New York and Desmond is under a tight deadline at the moment.

It's impossible to properly relive the memories of an ancestor of the opposite gender
Three games so far and all of Desmond's ancestors have been male, the Assassin's Creed multi-player scenarios do not seem to be proper memory revisitations. Plus, it makes a bit of sense since the Animus works on Genetic memory, the missing or added piece of a chromosome one ancestor had or didn't could make an enormous difference in synchronizing with an ancestor of the opposite gender.
 * Probably Jossed: in Brotherhood, Rebecca mentions having explored the memories of a Prussian mercenary who was one of her ancestors. She also said it was boring, which most likely eliminates any kind of Sweet Polly Oliver scenario.

The Assassins are actually the Delta Knights
Consider: Both are an ancient society of warriors who live in secret. Both are devoted to protecting ancient, advanced technology from those who would misuse it. Leonardo Da Vinci is a member of both. Also, look at their logos. The Assassin Insignia looks a lot like a very modified Delta.

The Six Vaults and their methods of Salvation
Jupiter stated that there were six vaults built, along with a main vault. He also stated that each vault was devoted to a different method of salvation. So what sorts of salvation methods do you think there were?
 * I think one of the vaults might be a gene bank of some kind. It wasn't designed to shelter any people, but rather to store genetic information of members of the First Civilisation so that they could be resurrected following the disaster and help rebuild the society faster than they otherwise would. The First Civilisation created humanity from scratch, so that requires some fantastic genetic knowledge. Therefore it's definitely possible that they could have a gene bank containing hundreds, if not thousands, of individual First Civilisation genomes. Think of the sheer amount of information stored in the titular ship in Titan AE, but probably more. Whether or not they've survived the 750 or so centuries since the disaster is uncertain.

Desmond is a mental patient
He's been diagnosed with severe schizophrenia and committed to the Abstergo Mental Hospital. Dr. Warren Vidic and Nurse Lucy Stillman are attending. He's been having increasingly vivid hallucinations of "past lives" while simultaneously losing more and more connection with reality. He sees his doctor as a cold bastard trying to subsume his "eagle vision" with drugs, and sees the more comforting Nurse Lucy and fellow patients Shaun Hastings and Rebecca Crane as his only friends in this obvious worldwide conspiracy against the "Chosen One," which is of course Desmond. He seems to even lapse into Borderline Personality Syndrome when he starts babbling more and more about some "Subject 16." However, when the good Nurse tries to administer Desmond a new drug, he suffers a severe psychotic break, overpowers and stabs her with the needle. The doctors are becoming increasingly convinced he's beyond help at this point.

The Assassins are just as bad as the Templars
All that talk about "working in the shadows to serve the light" is just that. Talk. The Assassins have their own agenda, and they are just as fanatically devoted to to is as the Templars are to theirs. The Templars believe in order and control. The Assassins believe in Free Will, and they believe it in so strongly that they will readily kill any leader who gains too much power over their subjects, regardless of how benevolent or well-intentioned they are. Both sides want the Pieces of Eden to further their own agendas. The Templars and the Assassins represent the opposing extremes of a spectrum of political philosophy; neither of them is the "good guy."

All of Ezio's love interests are Desmond's ancestors.
Ezio managed to have children with Rosa, Caterina Sforza, Cristina Vespucci, all the female Assassins, and who knows how many other women. Most of those children were likely taken away and raised by the Assassins (although Rosa could have easily just joined the order herself), and went on to have their own children. Desmond is the culmination of all their bloodlines.

The Legend of Zelda is a prequel universe to the series
Mostly supported by the [spoiler:Apple using a blinding light to kill people in the Brotherhood novelization] (I haven't played the game yet), and Din's fire from Ocarina of time having much the same power (Albeit much more subdued). However, I have expanded upon this a great deal since I realized the coincidence. The goddesses could be either prankster or benevolent Those Who Came Before, and the magical item in the games are pieces of Eden, the most obvious being apple and Din's fire, Papal Staff and byrna staff? Staff of byrna? I forget which, but it's the one makes you invincible. (Alternately, both the byrna, somoria, and pacci staves are all the papal staff with abilities limited by creativity and beliefs on what it can do.) the triforce is also a Piece of Eden, but more reveled because it was left behind by the goddesses in the presence of the king. The Assassins and Templars may or may not be pre-solar flare, though I'm pretty sure it's pre for continuity's sake and the whole "not being in the history books" thing is a lot easier to explain and would make for a more interesting psuedo-plot. Other expansions on this include wind waker and on being post-flare with impeccable timing, and the great flood was part of the Noah's arc thing. (please excuse my lack of biblical knowledge, I haven't read and my only church service was an easter concert with one sermon about not being a conspiracy theorist).

Lucy was working for Those Who Came Before.
While her reasons for the staged escape were good ones, her plan did have the minor flaw of giving the Assassins a shitload of vital information, something the Templars would be VERY hesitant to do. The truth is, she didn't care, because her real goal is to locate the Pieces of Eden so Those Who Came Before (or their successors) can snatch them all up. Why do they want them? Because they're planning to retake Earth, and they don't want the humans figuring out a defense against the Pieces of Eden.

Now that Lucy's dead, other agents (currently posing as Templars) will try to recapture Desmond. Aside from giving them access to Desmond's memories again, this will provoke the Assassins into an all-out attack on Abstergo, which will inflict heavy casualties on both sides. The only way to win is for the Assassins and Templars to ally. The Assassins have the genes that make them resistant to the Pieces of Eden, but only the Templars have the resources and familiarity with the pieces themselves to develop a true defense.

Oh, and that satellite launch? Yeah, that's just how the TWCB are snatching up the Po Es. They get the Templars to launch them into space, then the rocket explodes. The Templars assume it's Assassin sabotage, and the TWCB get the Po Es.