
The year is 2012. Desmond Miles worked as a bartender and is now imprisoned by Abstergo. He has the genetic memories of his ancestor Altair Ibn-la' Ahad in his DNA, who was a member of the 12th century Assassin sect during the Third Crusade. A machine called Animus searches his memory with the help of two scientists (Warren Vidic and Lucy Stillman). He gradually works his way through his ancestor's memories until he reaches the memory the scientists are searching for. The purpose of the abduction is the so-called "Piece of Eden" - a treasure, which the Templars (the play's main antagonists) found in 1191 under Solomon's temple. The Assassins have managed to retrieve it, and Altair must kill the Templar leaders trying to get the treasure back. As the play progresses, the nature of the treasure is gradually revealed. This seemingly worthless golden orb is gradually revealed as the object that "drove Adam and Eve out of Eden". It is then gradually revealed that this artefact is capable of deceiving the human mind and thus controlling people, and that it is not a divine or magical artefact, but a piece of extremely advanced and quite possibly alien technology. Desmond's captors eventually turn out to be the descendants of the Templars of today, who, as they did thousands of years ago, are trying to establish a new order using this artifact.
Source: https://cs.wikipedia.org/wiki/Assassin%27s_Creed_(s%C3%A9rie)

In the novel, the story of Altair is told by Niccolo Polo (father of Marco Polo) to his brother Maffeo during a visit to Masyaf (the seat of the Assassin order, author's note). Niccolo describes the life of an Assassin from his early childhood, through the indiscretions under the Temple Mount, the killing of nine targets, the restoration of the order, and the recovery of a treacherous artifact, in short, he sums up his entire life. The plot of the CGI version of the story is 80% identical in the novel, with the remaining 20% of the book consisting of parts that somehow that adds to or clarifies the story. After a botched quest, Altair, the head of the Order of the Assassins, is demoted back to novice and must regain his position. And he does so by, by killing nine designated targets to prevent a so-called "holy war". After a dispute between the Crusaders and Sultan Salah Al'din's men is settled, treachery comes from within the Order and the Assassin must deal with it. In the next part of the book, Altair leaves the Holy Land and makes his way to Cyprus, where he discovers the Templar conspiracy and tries to stop it. Next, the novel deals with the rebuilding of the Order of the Assassins and the upheaval from within the members themselves that could be devastating to the Order. Towards the end of the story, the reader feels compassion for the lives of Altair himself, who proves not only to be an excellent assassin but also a loving husband and father.
Source: http://www.comixzone.cz/view/1268-assassin-s-creed-tajna-krizova-vyprava