The overall story within Assassin's Creed is set in September 2012 AD. Desmond Miles, a bartender, has been kidnapped by unknown people (Abstergo) prior to the start of the game, and is brought to a building belonging to Abstergo Industries, where researchers are working on a project involving a machine called the Animus. The Animus is able to extract memories from the DNA of the user, passed on from descendant to descendant, 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 Ibn La-Ahad (?????? at-ta'er in Arabic meaning "Flying One" and his last name meaning "Son of the None"), a member of the Assassins Order during the Third Crusade of the Holy Land; the researchers express interest in understanding more of how the Assassins worked. Though initially Desmond's subconscious rejects the memories of Altaïr, he eventually learns to accept them and is able to proceed to follow Altaïr's actions through the Animus.
The memories of Altaïr that Desmond experiences start in the year 1191: Richard I of England has just recaptured the port city of Acre from the Saracens. 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 the Saracen forces are massing in 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 experiences is that of Altaïr, along with another assassin named Malik and his brother Kaddar, being ordered to retrieve a mysterious artifact from ruins of the Solomon's Temple in Jerusalem which is also being sought by The Knights Templar. As Altaïr and his companions make their way into Solomon's Temple, they discover that Grand Master of The Knights Templar, Robert IV de Sablé is also there. Altaïr attempts to kill Robert but, due to his arrogance and over-confidence, the ensuing attempt fails and Altaïr gets separated from his companions, leaving Robert and his men with Malik and Kaddar. Upon returning to the order's base of operation it is discovered that Malik survived the engagement; although losing an arm and his brother, he managed to retrieve the artifact. Since Altaïr failed to kill de Sablé, and for other offenses, The leader of the Assassins, Al Mualim stabs him. He awakens and discovers that Al Mualim has, rather than killing him, decided to give him a second chance. He is demoted to Uninitiated, the lowest rank in the Assassin Order (where Altaïr had started off when he had joined as a child) and is told how to rise through the ranks of the Assassin Order to his original rank: 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, helping the Order's goal of securing peace in the Holy Land.
Along the way, however, Altaïr discovers that his targets are bound by more than just a shared interest in personal gain, but are secretly members of the Knights Templar, with the goal to unite all mankind under a common cause. Desmond further learns by secretly reading emails on computers of the research personnel when left overnight between Animus sessions that Abstergo Industries is in fact run by the Knights Templar, the order having survived from the Middle Ages, and that the Templars are seeking the locations of several artifacts known as the "Pieces of Eden" that they can use to continue Templars' goals. Desmond learns that he was kidnapped so that they may learn, through Altaïr's memories, where the locations of the other Pieces of Eden may be buried throughout the world. He also finds that what remains of the Assassin's Brotherhood in modern days had tried and failed to recover him before that information could be learned. Altaïr's memories finally reveal that the assignment he undertook was a plot by the Templars to sow discord between the Assassins and the Crusaders and Muslims. In doing so, the Muslim leader Saladin and Richard The Lionheart would instead work together and fight the Assassins, and in the process, bringing peace for the Templars. Altaïr finally catches up with Robert de Sablé, his last assigned target, and defeats him. Robert de Sablé reveals in his dying words that Altaïr's master, Al Mualim, is also a member of the Templars, and he has now the sole power of the artifact, the "Piece of Eden" that is able to alter what men can see and can be used for mass hypnosis. Altaïr travels to face Al Mualim, who wields the "Piece of Eden", attempting to alter Altaïr's sight, but eventually falls to his 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, including two locations on landmasses that no longer exist in 2012 AD.
The Piece of Eden
The Piece of Eden
It is never truly explained how the "Pieces of Eden" were created, although Al Mualim says that water turning to wine, and various other miracles mentioned in the Holy Bible, never truly happened, but were all illusions created by people who possessed a "Piece of Eden". At one point, Desmond reads an email detailing the failed recovery of one other Piece of Eden and other unnamed artifacts, all resulting in disastrous accidents, including the Philadelphia Experiment and the Tunguska event. The email also refers to the Holy Grail, stating insufficient evidence to confirm its existence, and "Mitchell-Hedges Communicators", a reference to F. A. Mitchell-Hedges and his claim of Aztec crystal skulls that gave the owner the power of clairsentience. Further examination of the emails reveals some information regarding Earth as it is in the year 2012 AD. Africa and the United States have suffered calamities of various types; it is stated that an outbreak of L-11 disease has exterminated 96% of the African continent and the United States is facing unprecedented outward emigration, to the degree that the President of Mexico has stationed thousands of troops along the border, with monthly battles between American and Mexican forces resulting in over 300 casualties and 1,000 injured.
With Altaïr's memory complete, Desmond wakes up out of the Animus to learn that Abstergo Industries is already sending out recovery teams to locations shown by the "Piece of Eden" in Altaïr's memory, hoping to find additional artifacts. Desmond, no longer being of use to the Knights Templar, is to be silenced; however, he is saved by a researcher named Lucy Stillman, who reveals herself to be an Assassin by showing her hand with her ring finger closed as if it were missing. In the conclusion of the game, Desmond, having become "synchronized" with Altaïr, is able to use the eagle vision (a sort of empathic sight to see hidden messages and tell friend from foe) and by looking at Lucy, he can see that she is an ally to him (shown by her glowing blue as allies are seen by Altaïr), giving further proof that she is a genuine Assassin.
Cryptic messages on the wall of Desmond's bedroom at the end of the game.
Cryptic messages on the wall of Desmond's bedroom at the end of the game.
He also sees messages that only he can see, scrawled across the floors and walls that refer to the end of the world described by several religions, among other writings; such writings include references to the biblical passage Revelation 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, as well as part of a Mandelbrot set and other writings in foreign languages. There are many short messages including: Quetzacoatl's hunger lies the answers, I have entered the Abyss and never returned and a longer message reading: We are all books containing thousands of pages and within each of them lies an irreparable truth. At the top of the wall, near to the ceiling, the words "John's chapter judging sin and". Additionally, there is the Mayan date of 18.104.22.168.0—December 21, 2012 AD - the date on which the Templars' "new world" will begin, only three months away within the game's timeline and represents the planned date of the launch of a mysterious satellite the Templars have created, which they claim will "permanently end the war." The Arabic word "Az-Zalzala", literally meaning "The Earthquake" can be seen, which is the title of a chapter in the Qur'an that talks about Judgment Day. Some Nazca Line drawings are also found. There is also a reference to Yonaguni, a Japanese island similar to Atlantis. Also written on the wall of his room are the Hebrew words "Olam Ha-Ba" (???? ???), literally meaning "the world to come" and figuratively used to mean the afterlife. There are also a series of sayings and poems written in Chinese, most pertaining towards human action and reaction.
If used in the room with the Animus Machine, there are messages written on the ground that can be read by parsing the letters into words, starting with the bottom right letter and moving up, then to the next line left. The message close to the door that Vidic leaves by reads "Artefacts sent to the skies to control all nations to make us obey a hidden crusade. Do not help them". On the opposite side is a shorter message reading "They drained my soul and made it theirs. I drain my body to show you where I saw it", presumably meaning Subject 16 wrote these messages in blood. There are also many symbols, diagrams and drawings on the floor of the main room. There are several Nazca lines, a pentagram, rough sketches of a landscape, pyramids, pagodas and a Mesoamerican temple. There is also an Eye of Providence drawn near the door where Vidic left, above the cryptic message. There is a diagram of a triangle filled with eyes gazing up at a radiating apple, symbolizing the Tree of Knowledge. There is also an Eye of Horus in the corner of the room nearest to where Vidic left. The Emperor referenced on the wall in the bedroom is Jiajing of Ming China.
Further investigation after the credits reveals an email sent to Vidic by Lucy, stating that the drawings come from a mysterious "Subject 16" who went insane due to what they describe as a "bleeding effect" (essentially, genetic memory assimilation comes to a point where the subject can no longer distinguish between their life and their ancestors' memories).