[[WMG:Altaïr and Desmond are the same person.]]
The Apple let Alta´r cheat death by reincarnated as the person we know to be Desmond. This explains why Alta´r 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 Alta´r because the Animus is letting Desmond impose his face over Alta´r's in order to make him more comfortable in the Animus...which pretty much means we actually have no idea what Alta´r "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.

[[WMG: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.
** Desmond was born in an Assassin compound, where the majority of Assassins are descendants of Assassins. It's possible that Lucy is also the descendant of an Assassin, perhaps the female Templar.

[[WMG:The mysterious artifacts are actually from the future, they got sent back through time travel]]
So, TwentyMinutesIntoTheFuture, TheEndOfTheWorldAsWeKnowIt 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.

[[WMG: 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, [[spoiler: Confirmed but Desmond lost the skills from training after he ran from lack of practice.]]

[[WMG: 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 [[spoiler:Desmond]]. 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 in Revelations: Lucy was chosen to be an Assassin but later [[spoiler:betrayed the Assassins and joined Abstergo]].

[[WMG: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 [[spoiler:Vidic]] and [[spoiler:Lucy]]

[[WMG: 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 ChekhovsGun and/or an [[TheUntwist 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.

[[WMG: 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.

[[WMG: We've never seen Altaïr.]]
Sure, at first glance, Desmond is Altaïr's IdenticalGrandson. 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 [[GoodScarsEvilScars sexy scars]], just the dorky bartender.
* This is also stated very blatantly in the game.
** Thrown for a loop, though, with ''VideoGame/AssassinsCreedII''. 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 [[http://www.youtube.com/watch?v=Bf6Q1-YWAz4 gameplay trailer]] from ''Revelations'', where Ezio is the one reliving Altaïr's memories. He looks completely different.

[[WMG: 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 [[VideoGame/AssassinsCreedII ACII's]] release, and it was speculated that Altaïr was given an American accent in the original ''Assassin's Creed'' because [[ExecutiveMeddling higher-ups]] were worried that American audiences wouldn't take to a [[ButNotTooForeign 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''.

[[WMG: Everything Desmond was told about the Animus is wrong.]]
Looking through a persons life by reading their descendants "genetic memory"? A big case of ArtisticLicenseBiology. 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 GameplayAndStorySegregation from "It's an Animus abstraction!" into, well, GameplayAndStorySegregation.
** Also, cases of poor research and "You Fail X" are covered in the plot: why do the marks, real people we can look up in an 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 Creator/LeonardoDaVinci 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 {{handwave}}? Yes, but it's a very good one, because it's [[MagicAIsMagicA always consistent and an important plot point]], not just a random AuthorsSavingThrow.

[[WMG: The deaths of the Templars did not happen the way you see them in game.]]
After assassinating an individual you get to watch their FinalSpeech 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 BroadStrokes - 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 [[spoiler:that Animus is built by the Assassin's, so they wouldn't add things to justify Templar actions]].
* In this troper's opinion, the "memory" part of the assassinations extends only up to the moment the Hidden Blade lands on the mark's throat. During the {{final speech}}es, the entire background looks just like when you're about to be desynchronized, signifying that this part is outside of what actually transpired. Perhaps it's a glimpse of Altaïr's thoughts as his victim lays dying? There is a difference between recalling what happened in the past and reminiscing on what it felt like being there during that experience...

[[WMG: 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.
* Seems like an extension of the idea that you're desynchronized with every hit you take, implying that Altaïr was ''never'' hit even once.
* Confirmed, he swam (in a cutscene and we don't see him actually swimming but he jumps into the sea from a ship) in the DS/iOS game. The event was referenced in [=AC2=]'s codec pages.

[[WMG: Altaïr is OneOfUs]]
Obviously he played SuperMarioBros.

[[WMG: 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 [[http://en.wikipedia.org/wiki/Baphomet historical father of understanding]].

[[WMG: 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.

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

[[WMG: Disaster to be averted? Gamma ray burst.]]