The overall story within Assassin's Creed is set in September of 2012, where barkeeper Desmond Miles has been kidnapped by an unknown person prior to the start of the game, and is brought to Abstergo Industries, where researchers are working on the Animus project. The Animus is able to read memories from ancestors of the user that have been stored in DNA, allowing the user to replay those memories as if he were there himself. Desmond was "chosen" for the project due to his relationship to his ancestor Altaïr, a member of the Assassins during the Third Crusade of the Holy Land; the researchers express interest in understanding more of how the Assassins worked and reviewing a specific memory. Though initially Desmond's sub-conscious rejects the specific memory sought by the researchers, he learns to accept it by proceeding through the earlier memories leading up to it.
The memories of Altaïr that Desmond experiences start in AD 1191: Richard the Lionheart has just recaptured the port city of Acre from occupying Muslims. With a base of operations established, the Crusaders prepare to march south. Their true target is Jerusalem - which they intend to recapture for Christianity. However, Saladin, leader of the Islamic army, currently rules the city. Stinging from his army's defeat at Acre, he will not allow Richard to humiliate him again. The Muslim forces are massing in the ruins of Arsuf, intending to ambush the Crusaders and prevent them from reaching Jerusalem. These war maneuvers have left the rest of the Holy Land wide open. While Richard and Saladin battle one another, the men left to govern in their stead have begun taking advantage of their newfound positions of power. Exploitation, manipulation, and provocation rule the day.
The first memory Desmond experience 24524q167y s is that of Altaïr failing to assassinate the Grand Master of The Templar Knights, Robert de Sable, and recover the order's treasure. Due to this, Altaïr is demoted to Novice (the lowest rank in the Assassin Order). But Al Mualim, leader of the Assassins, offers him an opportunity to redeem himself. Altaïr must venture out into the Holy Land and assassinate nine men said to be exacerbating and exploiting the hostilities created by the Third Crusade. In doing so, he will stabilize the region, thus allowing peace to reign.
Spoiler warning: Plot or ending details follow.
Along the way, however, Altaïr discovers that his targets are bound by more
than just a shared interest in personal gain, but are in fact Templars
themselves, with the goal to unite all mankind under common rule. Desmond
further learns, from emails left overnight between sessions, and conversations with
his fellow captive, Lucy Stillman that Abstergo Industries is run by
modern-day Templars, who are seeking the locations of several artifacts that
they can use to continue the Templars' plans. Desmond learns that he was
kidnapped by the company so that they may learn, through Altaïr's memories, the
location of other artifacts like the Piece
of Eden, which was destroyed six years prior to Desmond's capture, in
Abstergo's Denver Facility. What remains of the Assassin's Guild in the modern
day, tries, and fails, to recover Desmond before that information could be
discovered.
Robert de Sable, the last of the men Altaïr kills, plans to unite the Crusaders and Muslims against the Assassins. In doing so, Saladin and Richard The Lionheart would instead work together and fight the Assassins, and in the process, bring peace. Altaïr finally catches up with Robert de Sable, his last assigned target, and defeats him. De Sable reveals, in his dying words, that Altaïr's master used him to destroy the others who knew of the Piece of Eden, which is capable of altering what men can see and can be used for mass hypnosis. Altaïr travels to face his Master, who wields the Piece of Eden, using it in an attempt a lethal misdirection, but eventually falls to Altaïr's blade. As Altaïr recovers the "Piece of Eden," the device activates one more time to reveal multiple locations across the globe in an holographic manner. With Altaïr's memory complete, Desmond wakes up out of the Animus to learn that Abstergo Industries is already sending out recovery teams to those locations, hoping to find additional artifacts. Desmond, now having no use for Abstergo Industries, was to be silenced. Lucy's intervention, claiming that he could be of further use, spared his life temporarily.
It is learned later that Abstergo is attempting to gain access to another 'Piece of Eden' so that they may use it against all of humanity. They plan to launch it within an orbiting satellite, set to launch on Dec 21, 2012.
In the conclusion of the game, Desmond, having become "synchronized" with Altaïr, and using Altaïr's eagle vision, and is able to see messages scrawled across the floors and walls, ostensibly written in blood, that only he can see, that refer to the end of the world described by several religions and other writings. Such writings include references to the biblical passage Revelations 22:13 ("I am the Alpha and the Omega, the first and the last, the beginning and the end."), a Lorenz Attractor, the Eye of Providence, the word Al-Zalzalah (الزلزلة) which is Arabic for The Earthquake which symbolizes the end of the world, and other writings in foreign languages. Additionally, there is the Mayan date of 13.0.0.0 - December 21, 2012 - which is also the projected date, on the Mayan calendar, for the end of this age of the world. The mysterious email (Titled "I KNOW") was sent at 13:00 (1:00 pm), though whether this is coincidental or not is unclear.
Spoilers end here.
Assassin's Creed is a game that has dual settings, one in the year 1191 during the Third Crusade where the player plays with Altair, and the other in a more modern era, between July and October in 2012 where the player takes control of Desmond Miles.
One subtle example appears in the high definition version of the Ubidays '07 trailer. Near the end, while the game's logo is visible, the screen glitches two different times. During each glitch, a single frame is displayed showing a molecular diagram. (To view this for yourself, click the Ubidays trailer link. Under the video click the Download link. Open the file with the appropriate player. Skip to 1:39. Then pause it and advance the video one frame at a time.)
Another example occurs during the demo at X06 (download the HD version here). At the end, after Altair dies, what looks like a side-scrolling menu appears with the following choices: "hard drive," "memories," and "options." Above each choice is the word "animus," which is Latin for mind or spirit. Below "memories" the phrase "access your genetic memory" can be seen.
The most interesting piece of evidence is from an interview with Kristen Bell (an actress whose voice and likeness will appear in the game), in which she states:
It's sort of based on the research that's happening now, about the fact that your genes might be able to hold memory. And you could argue semantics and say it's instinct, but how does a baby bird know to eat a worm, as opposed to a cockroach, if its parents don't show it? And it's about this science company trying to, Matrix-style, go into people's brains and find out an ancestor who used to be an assassin, and find out who that person was.
Ubisoft has confirmed that Assassin's Creed is part of a trilogy and has stated that one or both of the sequels may have a futuristic setting.
There is a Eye of Horus at one of the corners, in addition to three triangles,
two large and one small, resembling the Pyramids of Giza, possibly indicating a
sequel in Ancient Egypt.
Possibilities include sniping or very covert spying, requiring great patience to handle a lot of sneaking around.
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