As you remember, the final episode of the Assassin’s Creed leaves Desmond Miles, the kidnaped bartender in the hands of the Abstergo Industries. In the beginning of this episode, Desmond escapes the Abstergo headquarters with the help of Lucy Stillman, an assassin scientist that was working undercover at Abstergo. Together, they reach a safe house of the Assassins Order where along with other assassins, they continue the research that started at Abstergo.
Desmond enters a new Animus machine, much better than the one the Templars own. This time, the ancestor’s memories that Desmond enters do not belong to Altair, the syrian assassin from the Middle Ages, but to Ezio Auditore, a young italian boy from Renaissance Italy. Ezio is part of the Auditore family, a family that was well known in Florence for being bankers and close friends with Lorenzo di Medici, the leader of Florence. Ezio is a 17 year old boy who enjoys his life and often engages in fights with the son of the Pazzi family, Auditore’s rival family, Vieri. The memories of Ezio start when the young boy starts a fight with Vieri and defeats him. Because the authorities were coming, Ezio and his older brother flee the scene and go home.
The next day, Ezio receives from his father, Giovanni Auditore, some tasks to fulfill in his name. During these tasks, Ezio meets Leonardo da Vinci, a young scientist, engineer and artist. Ezio learns about a plot made by the Pazzis to kill Lorenzo di Medici. His father tries to expose the Pazzis but he is betrayed and killed by hanging with his other sons except Ezio. The hero is forced to leave Florence and he takes his mother and his sister away to Monteriggioni, where his uncle, Mario Auditore, was living. During his stay in his uncle’s house, Ezio not only finds out that his father was an assassin and that he was part of an old family of assassins, but he also learns and obtains the skills to become an assassin himself. Young and full of anger, Ezio returns to Florence to stop the Pazzi family and to save Lorenzo. Once in Florence, Ezio visits Leonardo who crafts for him the special weapon of the assassins, the hidden blade. Ezio starts his vendetta against the Pazis, eventually killing his old rival, Vieri. Ezio Auditore gets the respect and the support from Lorenzo when he saves him from death after being stabbed by Francesco de Pazzi, the head of the Pazzi family and then captures Francesco.
Later on, Ezio learns that the one who was actually responsible for the death of his father and brothers is actually the leader of the Templars, the Grand Master who’s identity was unknown. Moreover, Mario reveals to his nephew that they also need to find the missing pages of the Codex, a journal written by Altair long time ago. Ezio tracks down and kills other Templars until he finds the Master, who was Rodrigo Borgia, also known as the Spaniard. Borgia was one of the most powerful and most influent men in Europe and also a Cardinal at Vatican. Unfortunately for Ezio, he cannot kill Borgia. His clues and missions lead him to Forli, where he meets the countess of Forli, Caterina Sforza, who proves to be an important ally of the Assassins.
After the friendship between Ezio and Caterina becomes tighter, Ezio finds himself with Leonardo in Venice. Here, Ezio has to face new and much more terrible threats, since the Doge is working for the Templars. But also, in Venice, he makes new allies. During the Carnivale, Ezio infiltrates the Doge’s party and kills his important officers, eventually killing the Doge himself at his palace. One day, Ezio follows a group of important Templars who were meeting Borgia. While listening to their conversation, the young assassin learns that Borgia was expecting an important package that contained an ancient and powerful artifact. Moreover, he learns that Borgia was doing everything within his power to become Pope, which could have made him the most powerful man in Europe.
During an exchange, Ezio obtains the secret artifact which proved to be one of the Apples of Eden, one similar to the one Altair owned. Because of his success, Ezio meets Niccolo Machiavelli, who was also a powerful and influent member of the Assassin Order. Ezio is officially introduced in the Order. After collecting all the missing pages of the Codex, Ezio finds out about his next location, which was the Vatican. Ezio sneaks in the Sisteen Chapel attempting to murder Borgia, who was now the Pope. The fight against Borgia proves to be quite difficult since Borgia had the Papal Staff which was also a piece of Eden. Eventually, Ezio defeats Borgia but does not kill him, telling him that murdering him will not bring his family back. Ezio puts together the staff and the apple and reveals a secret temple under the Vatican, the Vatican Vault. Inside the Vault, Ezio encounters the image of Minerva, which at first seemed to be a goddess. Minerva tells Ezio that her message is not for him, so she will not speak to him, but through him. She starts her message by saying that her civilization was much superior to the civilization of men, and that her kind was the creator of mankind. Furthermore, she says that mankind raised a war against her civilization and because of this war they could not see that the end of both of them was near. The world was destroyed by flames, but together, the two civilizations reconstructed the world as they were build to survive. Minerva also says that only him can save the world from a new threat and then she mentions the name Desmond, leaving Ezio confused and his question unanswered.
The episode ends with Desmond and the other assassins leaving the safe house because it was compromised. While driving away from the safe house the assassins debate the message they just saw and reach the conclusion that Minerva was referring to the destruction of the world predicted in 2012.