Introduction
After the events on Assassin’s Creed: Brotherhood, Desmond Miles is trapped inside a coma due to the memories confusion that was created by the Animus between Desmond and his ancestors. Desmond’s mind wakes up inside the Animus where he meets Subject Sixteen (Clay Kaczmarek), Clay, who is also trapped inside the Animus, explains to Desmond that he needs to reveal the remaining memories of his ancestors to allow the Animus to perform Synch Nexus that solves the confusion and reawakens him from his coma. Desmonds begins to reveal Ezio Auditore Da Firenze memories by stepping inside a portal.

- The Portal -
Portal to the Past
Ezio is on his way to Masyaf, the homeland of the great Assassin Altaïr Ibn-La'Ahad, he seeks to find the knowledge left behind by Altaïr and gain more understanding of what he stands for. Upon arrival, he discovers that Masyaf is conquered by the by Templars who were able to capture him.
Ezio manages to escape, under the fortress of Masyaf he finds the entrance to Altaïr’s library, the massive door is locked with five keys, the keys are ancient artifacts that Altaïr used to record important memories of his life. Ezio learns that the Templars, who wish to find clues inside the library that lead them to a place called the Grand Temple, have already found one of the keys, he also learns that the Templars found a journal that reveals the locations of the other keys. Ezio manages to retrieve the journal of Niccoló Polo, the man who hid the keys throughout Constantinople.

- The fortress of Masyaf -
Ezio travels to Constantinople, a strange man called Yusuf Tazim welcomes him and accompany him around the city, Ezio finds out that Yusuf is the leader of the Assassins in Constantinople.
In his search for the five key, Ezio meets Sofia Sartor, an intelligent woman who owns a bookshop, working together, they discover the locations of the keys.
Keys of Memories. Memories of Keys
After finding each one of the keys, Ezio reveals one of Altaïr’s memories. the memories start with an invasion happened on Masyaf, where Altaïr managed to kill the traitor and save the leader of the Assassins, Al Mualim.
The second memory reveals the events that followed Al Mualim assassination by Altaïr, where Altaïr became the new leader of the Assassins and retrieved the Apple of Eden from Abbas who accused him of betrayal.
The third memory is about Altaïr arrival to Masyaf after 10 years along with his wife Maria, they found that Abbas has taken over the order and killed their son, Sef. Altaïr wanted to kill Abbas but Maria stopped him with her life, Altaïr was forced to escape.
The fourth memory is about Altaïr second arrival to Masyan after 20 years, Altaïr managed to kill Abbas and reclaim his place as a Mentor to the Assassins.
The last memory is about the keys when Altaïr handed them over to Niccolò Polo.

- Altaïr -
Constantinople Chaos
During Ezio mission to find the keys, he learns about the conflict between the Sultan’s sons, Ahmet and Selim, which one is more worthy to inherit the Sultan. Ezio meets Suleiman, son of Selim, who tells Ezio about his doubts about the conflict and the role that the Templars play in it.
In his investigation, Ezio discovers that one of the Templars, Manuel Palaiologos, is building an army in Cappadocia to revive the Byzantine Empire. Ezio follows Manuel and assassinate him but he discovers that Ahmet, son of the Sultan, is the leader of the Templars in Constantinople and he is the one after the keys.
Back to Constantinople, Ezio discovers that Yusuf has been killed and Sofia was kidnapped by Ahmet and his men, Ahmet wants the keys in exchange for Sofia. Ezio saves Sofia by handing over the keys, but then he chases Ahmet and retrieves the keys. Before he assassinates Ahmet, Selim arrives with his army, he informs Ahmet that the Sultan has chosen him (Selim) to be his inheritor, and then he kills his Ahmet. Then Selim tells Ezio to leave Constantinople and never come back.
- Yusuf death -
Reawaken in the Animus, Desmond finds all the data is being deleted, Subject Sixteen sacrifices himself to save him by pushing him into the portal just before the deleting.
The Revelation
Ezio returns to Altaïr's library in Masyaf along with Sofia, he enters the library, inside he finds only the skeleton of Altaïr setting in the middle and a new artifacts in his hand, the artifact reveal one last memories of Altaïr locking himself and the Apple of Eden inside the library, Ezio decides to leave the Apple locked away, after that Ezio directs his speech to Desmond, telling him that he feels like he has fulfil his purpose.
Desmond find himself in a strange place where he meets Jupiter, one of those who lived in the first civilization, Jupiter starts to tell Desmond about what happened to the first civilization where humans and -the ones that came before- lived, they were consumed by war and didn't notice that the end of the world was drawing near. as an act of emergency -the ones that came before- built vaults each one with a method of salvation, they tried six methods but none of them worked, the time was running out, so they sent all the knowledge from the vaults to one central vault (Also known as the Grand Temple). Then the disaster occurred , only 10,000 humans survived and very few of -the ones that came before-. After that Jupiter reveals the location of the central vault to Desmond.

- Desmond and Jupiter -
Desmond awakens from his coma, he tells his companions, Rebecca, Shaun and his father William that he knows what to do next.

