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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?

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.
    • Did you even play the end of the game? To talk to Desmond, Minerva looks at the camera, not Ezio, proving, at least, that people in the Animus actually experience their ancestor's memories in third-person. Also, seeing as they're the first humans, wouldn't everyone have genetic memory of Adam & Eve?
      • No, Adam and Eve weren't the first humans in the AC universe. If you actually watch The Truth video, you'll see plenty of humans under the enslavement of The Ones Who Came Before via the Pieces of Eden. Adam and Eve were the first hybrids of humans and The Ones Who Came Before, hence why they were immune to the Apple's control and they possess TOWCB's extrasensory abilities. The Assassins and Templars are directly descended from them, though their blood flows most strongly through Desmond.

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.

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.
  • Confirmed, sorta. There is no one after him to fight, as there was with De Sable in A C 1, because he has gotten control of another Piece of Eden.

Assassin's Creed and RahXephon 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 RahXephon, 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 an Evil Plan 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.

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.

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.

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 Minerva does the whole Breaking the Fourth Wall thing with Desmond, with what appears to be remarkably specific knowledge of what will be happening over 500 years into the future. This level of precognition seems out of place for a race that failed to see its own destruction coming, but notice that at the beginning of the scene she asks Ezio to show her the Apple, and then almost immediately after this briefly turns to face the camera for the first time. 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 pole shift and the resulting destruction, something the Precursors predicted. It's not an actual vision, just a warning of what's to come.

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 the human race was made by a precursor race that left behind Pieces of Eden and after their demise, memories of them became the foundation of mankind's worship of gods. Looking at one of the glyph puzzles, concerning the origins of Assassins, all the relevant clues to solving the puzzle involve paintings depicting mortal women having sex with gods. 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.

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.
  • While this would certainly be one hell of a plan 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.
" 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.
  • 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.

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. 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 Wave}} Handwaving]] 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 See hundreds of different Animus, and in Brotherhood the Multiplayer revolves around Templars using Animus to train against the Assassins.

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.

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
    • But the theory is jossed by Brotherhood and Revelations, which both feature Ezio saying that he heard Desmond's name from Minerva.

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.

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.

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.

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.

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.
    • Perhaps because Ezio is shown to be young, and to be honest, relatively stupid at times. His father may not have trusted his judgment yet. Although that does raise the question as to why Petruccio knows...
    • Ezio was a very... "sociable" man in his younger years. Most of his time was spent outside the home. Petruccio however was (almost) always at home because of his sickness. Also Petruccio should be able to use eaglevision so it wouldn't be to unlikely that he someday spotted the hidden door where Giovanni had his assassins robe and stuff. He then pressed his father on the subject and maybe first he was reluctant to tell him, but since he has proven that he could find out that his father secret on his own he perhaps felt he could rely on Petruccio to also keep it. Perhaps he also had the intention to make him a no-action assassin.

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.

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: Ezio settles down with a new woman, Sofia, in Revelations. Desmond is descended from that relationship. Although there's still a possibility that Ezio and Rosa had a kid on the side we never saw.
  • New theory: Subject Sixteen is descended from Rosa.

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

Rosa is Vin
  • 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:
    Jump implausibly high and scale tall buildings
    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.

Rodrgio Borgia was able to will the Apple of Eden from Cyprus into existence by sheer greed

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.
  • I'm making this my fanon.
  • But then what was the point of him?

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