“Better in the hands of the Earth, than in the hands of man.”
“What can I say? We sent one man against an entire army. I was worried. Quick, climb up. We have to get out of here.”
“You would not believe the things I have seen, Mario”
“Then be sure to stay alive, that I might hear them.”
“I expect opposition.”
“And I expect the Borgia to mourn the loss of many lives tonight.”
As Ezio and his uncle Mario hurry out of the Sistine Chapel with the Piece of Eden, they are unsure what to do with it. So they take it back to their hideout in Monteriggioni. Once there Ezio does not lose any time to impress the ladies, retrieve his uncle’s runaway horse, and try the new cannons. Although Ezio is most keen to see Caterina once more, his first task is to tell his fellow assassins of his fight with the pope, who at the time was Rodrigo Borgia, and the apparition of the goddess Minerva to warn humanity about the end of the world. Machiavelli is shocked to hear that Ezio has let Rodrigo live, but anyway Ezio now just needs a rest and a warm bath, and Caterina decides to lend a hand.
After sleeping with Caterina, Ezio wakes up in the morning among the blasts of cannon fire. The villa is under attack by the Borgia and the Piece of Eden is the stake. He quickly puts on his clothes and prepares to fight. Almost getting hit by a cannonball, the assassin climbs to the ramparts to fire one of his own cannons back at the enemy.
Ezio buys enough time for the villagers to flee, but the gate is breached and uncle Mario lies lifeless on the ground. The enemy leaders come inside the fort, and Cesare Borgia is holding the apple. He shoots Ezio and calls his men to attack. Ezio, hurt but still on his legs, searches for his sister Claudia and leads her to a secret escape through an underground tunnel. He then hops on a horse and tells his mother and sister that he is leaving for Rome.
In the present day world, Lucy, Desmond, Shaun, and Rebecca are also on the run. They drive to the villa and set up their base there. They know that Ezio hid the Piece of Eden in 1507, but they are still trying to find out where by means of Desmond and the Animus.
It is a new year in Rome. Ezio gets back on his feet after falling down from his horse due to his injuries on his way to the big city. He is carried to a safe place by a mysterious person, and instructed to meet Niccolò Machiavelli at the Mausoleo di Augusto. After a quick visit to the doctor, Ezio goes to his destination where Machiavelli leads him to the nearest blacksmith to fit him with a dagger. He then tells Ezio that Cesare Borgia is building a huge army in order to have all Italy under his control.
Ezio is the kind of man that does not bow to the Borgia’s power so easily. He kills one of their captains and burns the Borgia tower in order to free the people from their will. Ezio suggests that he will free the people of Rome by reducing the Borgia’s influence over the people, but Machiavelli is not too impressed. He asks Ezio to get a letter for him, but on his way back Ezio meets the cult of the Followers of Romulus, dressed in wolf hide and looking for a fight with the assassins. Ezio goes to investigate their hideout to find out that a special armour is protected by six locks that must be opened in order to find the cult’s secrets.
At the end of the day, Machiavelli takes Ezio to their hideout on Tiber Island and introduces him to Fabio Orsini, the place’s owner. Here Machiavelli tells Ezio that their situation is desperate. The Borgia have too much power in the city. The assassin-run brothels, which are usually a good source of information, are lacking, and the guild of thieves are not collaborating with the assassins. Ezio steps up and starts making some changes.
Whilst the modern day assassins plan their next move, Ezio goes to pay a visit to the local brothel, the ‘Rosa in Fiore’. He finds out that the owner was taken hostage by a group of slave traders, so he tries to negotiate with them at the port, but they just kill the lady. When Ezio returns to the brothel to bring the grim news, he finds his mother and sister there waiting for him. With no one to run the business, his sister Claudia takes it upon herself to manage the brothel, with some monetary aid from Ezio.
Next, Ezio goes to find his old friend Bartolomeo D’Alviano, who Ezio helps to eliminate the Borgia threat near his friend’s barracks so that he can concentrate on the campaign against the French. In return, Bartolomeo pledges his mercenaries to spy against the Borgias. A while later, Ezio meets Machiavelli in front of Castel Sant’Angelo which he plans to infiltrate to kill Cesare and Rodrigo. At that moment they see Caterina Sforza being dragged in public, with Lucrezia Borgia making a show of her. Ezio starts his mission, climbing inside the castle’s walls
Inside Sant’Angelo, the assassin overhears Cesare plotting against his own father with his allies and then observes him as he kisses his sister Lucrezia passionately. Ezio is in luck however. Cesare leaves for Urbino, leaving the castle without a leader and an excuse for Ezio to free Caterina instead of killing his mark. He finds her locked in a cell, and spots Lucrezia going away with the key.
Since obviously Lucrezia refuses to hand the key over to the intruder, Ezio forces her to come with him and open the cell herself. Caterina is too happy to take away the key from Lucrezia’s dress and exchange places with her. She is injured though and cannot walk too far, so Ezio has to carry her out of the castle. At that point, Caterina asks him why he came to save her, explaining that she only slept with him in order to get the assassins to protect her family.
During this time, Ezio starts to reminisce about his past, about his goofy attempts to charm Cristina Vespucci, his fights with Vieri de Pazzi, and the execution of his father and brothers. But now there is a more important matter at hand, to take Roma away from the Borgia’s influence. Ezio’s plan is to free the people from their oppressors and recruit them as assassins with his new brotherhood. The liberation of Roma has begun.
Ezio starts using his newly-recruited assassins to eliminate people like Doctor Malfatto who is terrorising the local whores, and Silvestro Sabbatini who is also trading slaves. He also sends his recruits across various missions around the world in aid of the assassins. Soon after, Leonardo da Vinci comes to visit his old friend. He tells Ezio that he was forced to do some work for the Borgia. In fact he has designed some war machines for them, which Ezio must now destroy. On the bright side, Leonardo will also help by designing and building new weapons for the assassins.
The assassins assemble to plan their next move. They know that Cesare’s army is being funded by someone just known as The Banker. It is decided that they must get him out of the way. The tip is that Ezio has to find a senator called Egidio Troche, who will lead him to The Banker. He goes to the Campidoglio and is just in time to see the Borgia soldiers holding the old senator and demanding money from him in The Banker’s name. Ezio nimbly disposes of them and gets to the matter of getting his answer, but they must go to a safe place first. Back at his brother’s home, Egidio reveals that he owes money to The Banker because of his gambling habits, but he doesn’t know where he can be found. He tells Ezio that what he usually does is to go in one of three places, and wait for the guards to escort him to their master.
Ezio has a plan. He gives the sum of money that The Banker is requesting to Troche and sends him to deliver it. Then he follows him in the shadows. The guards take the senator to the Pantheon, and the leading guard goes inside with him to count the money. Ezio takes the opportunity to sneak in, kill the leader and take his place to deliver the money to The Banker. Ezio arrives to his destination at the Trastevere. A huge party thrown by the banker welcomes him. Another guard takes the chest of money from Ezio to personally deliver it, so the assassin has to again make his way in stealthily.
What a surprise: The Banker is none other than Cardinal Juan Borgia. And there’s even more: Cesare and Rodrigo are at the party too, the former is giving a speech about his conquests throughout Italy, and the latter is not too impressed. What is less of a surprise: one dead banker ends up lying down on the cold stone floor, and Claudia’s courtesans take Ezio’s money back .
After a trip to Napoli to destroy Leonardo’s naval war machine and design, Ezio returns to the matter at hand. Bartolomeo needs help because Cesare has convinced King Louis of France to send an army to crush him. The army is being led by the Baron de Valois, who makes the first move by trying to capture Bartolomeo’s barracks. The frenchman is holding his wife Pantasilea as hostage, and demands his surrender before night. Bartolomeo almost loses his hope, but Ezio has an idea.
Ezio’s plan is to infiltrate their enemy’s fortress disguised in french armour, and he is the one that will steal the goods. Once he kills enough soldiers, Bartolomeo’s men pillage their belongings and prepare their surprise for the baron. The fake frenchmen take Bartolomeo to surrender to the baron, when they spring their trap. Valois manages to run away and holds Pantasilea at gunpoint, but Ezio manages to kill his mark and save the lady.
Ezio’s old friend La Volpe tells him that he suspects that Machiavelli is giving information to the Templars, but Ezio does not believe it. The Borgia seem to know their every move, and tonight they plan to murder one of Volpe’s thieves. They quickly take action and ride to find more information in order to save him. They find out that the plan is to kill a man named Pietro, who is participating in a play as Jesus, because of an affair with Lucrezia. The task will be executed by Micheletto, who will strike once Pietro is hanging on the cross.
The play is being held at the Colosseo. Ezio must get to Pietro before Micheletto does, and again his plan is to mingle with the crowd as an actor and get dressed as a Roman soldier. After finding a way in through the structure’s corridors, Ezio manages to hold back Micheletto from hitting Pietro. However, Micheletto is an experienced killer as well, and he has made sure that he succeeds by poisoning his target during the thirst scene. Ezio takes Pietro quickly to the nearest doctor who gives him an antidote. There he sees one of his own men from the villa, but when he greets him the man runs away. Ezio follows him and once he catches up, he discovers a letter from the Borgia that reveals that the man is a spy. Ezio takes the letter to Volpe as a proof that Machiavelli is innocent.
Volpe reveals to Ezio that now the papal and french armies are in disarray. So Ezio decides to assemble the assassins, and welcomes his sister into their ranks. Just then Machiavelli also announces Ezio as their new leader and gives him the title of Mentor. His first decision: eliminate the Borgia! And their friends the followers of Romulus.
Ezio is soon outside the Castel Sant’ Angelo, getting ready for a personal meeting with the pope. Interestingly, Cesare just came back as well. It’s Ezio’s favourite pastime; climbing the castle’s walls, sneaking through the shadows and occasionally killing some hapless guard or two. As Ezio finally gains his way inside the castle’s walls, he observes Rodrigo and Cesare having an argument about the pope not funding his son’s campaigns in a suitable way. Lucrezia bursts in, and tells her brother that the apples on the table are poisoned, prepared for him by their father. Cesare forces his father to bite one, and demands to be told the whereabouts of the apple of Eden. However, Lucrezia tells him that she knows where it is hidden as well.
Cesare is not interested in his sister’s affections, only by the power that the apple will give him. So he goes off to take it. Meanwhile, Ezio climbs through the room’s window. Lucrezia also tells him the location of the apple, so he hurries along to beat Cesare to it. With the apple back in his hands, the assassin is able to bend the will out of his opponents and not even Cesare is able to confront him.
With the pope dead, Ezio now returns to the hideout with the apple in order to plan the assassins’ next move. He waits for Cesare to assemble all his men together, and repeats his apple trick once again to leave his enemy without an army. A month later, he foils Cesare from getting any aid from the church. By year’s end the assassins have ousted Cesare outside the city’s gates, and to add insult to injury the new pope’s army has him arrested and taken away.
Ezio is worried about what Cesare said before he left. That no chains will hold him, and he cannot die by hand of man. Leonardo suggests to use the apple in order to reveal the truth. At first Ezio hesitates, but then his curiosity takes the better over him. As soon as the assassin touches the apple, he gets up from his chair and leaves at once.
In the fortress town of Viana, Ezio seeks to finish his job. Cesare had escaped from his Spanish prison to help his cousin who has now given him a new army to conquer the town. And Ezio now rides across the battlefield while Cesare’s siege weapons wreak havoc against the defenders. A bomb blast forces his horse to the ground. So Ezio continues on foot, but the main action is close now. He manages to climb a siege tower in order to gain access inside the town’s castle.
Cesare’s army is gaining the upper hand on the defending army at this point and he is busy showing off his master swordplay. Just then Ezio shows up and demands his enemy to stop running away. Cesare obliges, confident that he cannot lose. Ezio must practically fight with Cesare’s whole army while he tries to land the killing blow against the Borgia General.
At last Ezio manages to leave his opponent powerless. Cesare once again repeats the prophecy that he cannot be killed by any man. So Ezio holds him in mid-air at the top of the ramparts, tells him that in that case he will just leave him in the hands of fate, and lets go. Unsurprisingly, Cesare drops down to his doom.
After completing his mission, Ezio returns to Rome and hides the apple inside a vault in the Colosseum. Lucy and her team are able to see him through the animus, but they need a password. Through his acquired eagle vision, Desmond manages to find a symbol that reveals the required key. So they quickly go to their destination, and Desmond is the only one who can make his way through the structure’s walls right to the basement. There he is greeted by the ethereal appearance of the goddess Juno, but he does not reveal it to the others.
As Desmond moves on, Juno, like Minerva before her, recounts the history of the world and her species’ interaction with man. And seemingly similarly bitter about it. Desmond finds a way back up inside the church of Santa Maria, where the others are waiting outside for him to open the door. He lets them in, and like his ancestor, Desmond’s instincts lead him to climb the walls towards the church’s ceiling. A switch opens a secret passage on the other side, and the modern day assassin shimmies along with Juno still filling up his mind with her words of wisdom. Then some strange contraption pops out of the floor.
As Desmond touches the contraption, it lights up and the ground below him and his bewildered colleagues starts sliding down to a level below the ground just as if it was a lift. They end up in Juno’s temple, where old structures are mixed with panels containing futuristic imagery. Desmond says the password, and a door opens to lead them inside another hall. The apple is within their range of sight, but again it’s not a simple way up. And again, Juno chooses the right time to fill him in on some more history.
When Desmond is within touching distance of the apple, magical symbols start appearing all around out of thin air. He picks up the Piece and Juno speaks about the special day that humanity was born from them and their enemies. She speaks about the final journey and other riddles about a woman who is not within their vision. The goddess then tells Desmond that he must be guided, so she takes control of his body to strike Lucy with the hidden blade. Then she instructs him to go and find the sixth sense of knowledge, which is when both he and Lucy drop down unconscious on the floor.