Assassin's Creed is the story of Desmond Miles.
A (presumably) twenty-something bartender, Desmond wakes up one day to find himself strapped to a metal table of sorts. He has no recollection of how he got there, but he is being held captive by two scientists - Dr. Warren Vidic and Dr. Veronica Mars - that work for a scientific corporation called Abstergo Industries.
Vidic reveals to Desmond that the scientific team at Abstergo has uncovered the fact that memory is stored in DNA. So when you die, your memory will be implanted somewhere in your child's DNA, you have your father's memories in your DNA, so on and so forth. This accounts for "animal instinct" in lower life forms, such as the migratory patterns of birds in the winter. Bad news for Desmond, they reveal that not only do they know that Desmond was raised since birth to be an Assassin, but he is also the descendant of an Assassin who knew information they considered vital. Seeing as death sucks pretty badly, Desmond has to comply and be hooked up to a machine that will allow him to remember the life and times of an ancestor in 1191 Jerusalem, an Assassin named Altair. (Editor's Note: Altair means eagle. So does Ezio!)
In Altair's memories, he's kind of a dick. There are three simple rules to being a good assassin (a creed, if you will) and he manages to horribly fuck up all three in the span of one mission and also fails to kill his target, but yet we are led to believe that Altair was valedictorian of the Assassin school. Anyways, he kills an innocent, is not very discreet, and compromises the brotherhood. He tries to be a cock and lie about it, but one of his clan members exposes him, and also brings the treasure that they were sent to retrieve, effectively upstaging Altair. In retaliation, the target who was supposed to be dead, Robert de Sable, leader of the Knights Templar, leads an attack on the Assassins.
The Assassins are successful in defending their home. However, to make an example out of Altair and punish him for his terrible behavior, his clan leader, Al Mualim, fake-stabs him for some reason but then tells him that he can make up for his transgressions after all. I never really got the whole fake-stabbing thing 'cause it's not like he secretly
let him live, all the Assassins you meet afterward are all like "Oh hey Altair! You're a pretty cool guy."
, Al Mualim is all like "Hey, there are nine bad men out there. Kill them and you'll no longer be a novice. Also you'll remember some of the physical abilities you magically forgot when I demoted you." Since Altair lacks a personality and doesn't really have much else to do anyways, he agrees out of sheer boredom. Altair traverses through the three cities of Jerusalem, Damascus and Acre, picking off the nine targets one at a time. Upon meeting their end, each has time to give lengthy speeches that sometimes bores to tears and always successfully freeze time; upon the instant of their death, time unfreezes and guards start attacking.
They all say vague, cryptic things, and when Altair confronts his master about this, he spits out vague, cryptic things. Upon assassinating Robert de Sable, his target reveals that Al Mualim himself is a member of the Knights Templar. Altair confronts Al Mualim with this accusation, who responds with a resounding "Well duh
." He then brings out the treasure that was retrieved (by the lesser student) in that first mission that Altair botched, and reveals it to be a "Piece of Eden", which is apparently good for mass mind control in addition to looking pretty nifty. Remember when Bright Eyes parted the Red Sea so that he could let his people go?
Impossibilities like that (also the ten plagues of Egypt and Clash of the Titans) were apparently caused by the kind of mind control this thing delivered, so obviously it was being fought over by these two powerful groups of Assassins and Templars. Tired of the manipulative dickery he had been subject to his whole life, Altair shanks Al Mualim and takes the Piece of Eden. At which point, a holographic map shoots out of it and shows the locations of the other pieces.
This is the memory that Abstergo was looking for. After they retrieve the memory, Vidic tells Desmond he was ordered to be killed, but Veronica saves his life by claiming that they might still have more use for his memories. Vidic reluctantly agrees, and Dr. Mars looks at you and bends her ring finger down, a gesture showing that she's on your side (Assassins in the old days would have their ring fingers removed because they were fucking hardcore). As Desmond is left alone, he finds that he has received a new gift; he knows kung fu. Not really, but he can see stuff in Dayglo vision, which is also handy, as it lets him see stuff that is incredibly well-hidden and also reveals enemies and allies. As the game closes, he goes back to his room with his newly acquired skill and sees the walls covered in a bunch of crazy shit: a bunch of symbols on the wall all alluding to the end of the world on December 21, 2012.