Last time we met with Desmond Miles and his adventure of finding the secrets of his ancestors was in Rome, when he kills Lucy against his will and where he falls into a state of coma. In this episode, Desmond will be entering once more in the memories of Ezio Auditore.
After Lucy’s death, Desmond is taken by his fellow assassins to New York where they meet Desmond’s father, William. With the help of William, Desmond is placed again into the Animus, hoping that he will wake up. Desmond is placed in the safe mode of the Animus, a place called Black Room. There, Desmond meets Subject 16, a former assassin that like Desmond, was a subject for Abstergo‘s research and because he used the Animus for too long, he became insane and remained stuck into the Animus. There, Subject 16 tells Desmond that in order for him to get back, he needs to find a key memory that will synchronize him with both Ezio and Altair, his ancestors.
Desmond enters Ezio’s memories once more. This time, we meet a different Ezio, older and much wiser. 30 years after the death of his father and brothers and after the defeat of the Borgias, Ezio travels to the Middle East to find out the secrets and knowledge that Altair left behind and to find the true purpose of the Assassin Order. The italian reaches Masyaf castle, the place where the Order was rebirth and where Altair hid all of his secrets only to find out that the place was overrun by templars that were also trying to find the secrets. Being overrun, Ezio is captured by the templars but manages to escape when they were trying to hang him. Fighting his way through the castle, Ezio finds Altair’s vault beneath Masyaf but the entrance was sealed and the keys required to open it were nowhere to be found. The assassin learns that 5 disc-like keys are supposed to open the vault and that those keys were hidden in Constantinople. Ezio travels to the capital of the Turkish Empire where he meets Yusuf Tazim, a turkish assassin, leader of the assassin clan in Constantinople. Also, he meets a young student called Suleiman and they become friends. Learning more and more about the city, he also finds out that the keys were hidden here by Niccolo Polo. In this city, Ezio meets Sofia Sartor, an italian traveler that helps Ezio in finding the keys of Masyaf. Ezio falls in love with her but keeps his feelings secret from her.
Constantinople was a battlefield between Prince Ahmet and his brother Selim who were fighting for the title of Sultan. Suleiman reveals to Ezio that he is an ottoman prince and he believes that the templars are behind this war. After many fights against the templars, Ezio recovers most of the keys. These keys are synchronizing Desmond with memories of Altair. The first memory of the syrian assassin is right after he kills Al Mualim and he retrieves the Apple of Eden. Altair takes the Apple and Al Mualim’s corpse and burns it in order to make sure that the mentor was dead. He is called a heretic and a defiler by the other assassins and Abbas, Altair’s companion, takes the Apple from him but loses his mind when he tries to control it. Altair takes the mantle of Mentor of the Assassin Order. He is forced to leave Masyaf several times in order to stop the Mongol attacks and during his absence, Abbas takes the leadership of the assassins. Abbas, jealous of Altair, betrays him when he refuses to send more troops in order to aid him in the battle against the Mongols and this results in the death of his youngest son. Altair and his wife Maria, encounter Abbas to demand an explanation. Abbas asks for the Apple in exchange for answers and during the exchange, Maria is stabbed by another assassin and Altair is forced to leave with the Apple and his older son Darim. The two syrians go in an exile for 20 years. During this period of time, the Order suffers of corruption under Abbas’ leadership. After 20 years, Altair returns to Masyaf where he kills Abbas and takes the title of Mentor over the Order.
Back in Constantinople, Ezio finds that the leader of the templars was actually Prince Ahmet and he was the one behind the operations of retrieving the secrets of Masyaf. After killing Emanuel Palaiologos, a templar knight, Ezio recovers the last key of Altair’s library. Ahmet kills Yusuf and kidnappes Sofia and will only release her in exchange for the keys. Ezio gives him the keys and saves Sofia. After a struggle, Ezio recovers the keys from Ahmet but before he can kill him, Selim arrives with his army and executes Ahmet. Because of his friendship with Suleiman, Selim orders Ezio to leave the city and never return. Furthermore, Ezio and Sofia travel togehter to Masyaf to open Altair’s Library. On their way, Ezio explains to Sofia about the creed of the assassins, that “Nothing is true, everything is permitted“. He explains that this is not a doctrine, it is merely an observation of the world. To say that nothing is true means that the foundations of society are fragile and we must be the shepherd of our own civilization; to say that everything is permitted means that we should live with our choices, wether glorious or tragic. Sofia also asks Ezio if he regrets choosing this life; Ezio answers by saying that this life chose him and that for the last 30 years he fought for the memory of his loved ones but that this was the time for him to live for himself. Ezio walks alone in the library; there he finds no books, no wisdom, just the corpse of Altair himself. Once again, the memories of Desmond, Ezio and Altair synchronize. In this memory, and old Altair gives instructions to his son Darim. Darim is confused that his father build a library in which he will not keep his books but he realizes that this place was actually a vault in which Altair was hiding the Apple. Altair tells Darim to take some keys to Alexandria and tell Niccolo Pollo to take some keys to Constantinople. Moreover, the assassin tells his son that if he is asked, he must tell that he send the Apple away or that he dropped it into the sea, he tells him to say everything to keep the people away from Masyaf (the assassins were leaving Masyaf because the Mongols were too strong for them). After these instructions, Altair sends Darim to go and live with his family. Inside the vault, Altair remembers of voices from the past, discussions with Maria about the images the Apple was showing him, about the ones who came before. After hiding the apple into a safe, Altair takes a seat in the middle of the chamber, the same seat where Ezio finds his corpse. Ezio opens the safe, but does not take the Apple, stating that this is the safe place for this artifact and that he has seen too much for one life. Right after this, the Apple activates, and Ezio hears Desmond’s name again. Stripping off of his weapons, Ezio says that it is clear to him that he is only a messenger in this fight and that he does not know how Desmond is listening or watching him but he hopes that Desmond will be the one to find an answer for their suffering.
After this synchronization, Desmond is approached by Jupiter, a being that was part of the ones who came before, same as Minerva and Juno. Jupiter tells Desmond that the First Civilization has created numerous vaults around the world where they were collecting data in order to save the world from destruction. All the data was gathered to a central vault where the data was tested but no results were gained. They failed in protecting the world from a solar flare and so most of his people died. After the destruction, 10,000 of Desmond’s kind were still living and far less of Jupiter’s but the world was rebuild by them together. Jupiter warns Desmond that the world was in danger of a second solar flare and that he must find a way to save the world this time; moreover, Jupiter shows him the location of the central vault. After the final vision, Desmond finally wakes up from his coma and states that he knows what the assassins need to do. The game ends leaving the audience in a confused state and also believing that the next game will present the ending of this story.