Dealing with the Borgia

Confrontation in the Vatican

"I thought... I thought I was beyond this. But I'm not. I've waited too long, lost too much."

―Ezio to Rodrigo during his first assassination attempt.

The following year saw the Assassins come together once more at the Villa Auditore, with the Piece of Eden and the completed Codex in hand. Using the two objects, they discovered the location of the Vault to be in Rome - specifically, beneath the Vatican.
Unfortunately, Rodrigo Borgia had become the Pope in 1492, although Mario believed he had only done so to gain access to the Papal Staff, another Piece of Eden. Undeterred, Ezio went to assassinate Rodrigo.

Ezio confronting Rodrigo in the Sistine Chapel

Fighting his way along the entire length of the Passetto di Borgo, Ezio snuck into the Sistine Chapel and struck at Rodrigo from above.
As he was about to deal the killing blow, Rodrigo surprised Ezio by using the Staff of Eden to blast him away, and drain the energy of those in the room. Since Ezio held the Apple, he was immune to the Staff's effects, and the two engaged in a duel.
Ezio created multiple illusional copies of himself with the Apple. For a while, it seemed that Ezio had bested Rodrigo, but the Pope overcame him. Rodrigo then took the Apple and stabbed Ezio in the abdomen, leaving him to die before fleeing towards the Vault.
However Ezio soon regained consciousness and, following his nemesis to the outside of the Vault, Ezio watched as Rodrigo tried in vain to open it. Laying down his arms, Ezio challenged and defeated Rodrigo in a final brawl, obtaining possession of both the Apple and the Staff. However, he refused to take Rodrigo's life, having realized the futility of revenge.

Minerva appearing before Ezio

Entering the Vault, Ezio stood in shock as he was confronted by a hologram of an individual naming herself Minerva, and claiming to be one of "Those Who Came Before".
Ezio was further confounded when the hologram spoke to an unseen figure named Desmond, and started showing holograms of an event that would befall the world hundreds of years from then. Minerva then disappeared abruptly, leaving Ezio with many unanswered questions.^[1]
Ezio left the Vault and met up with Mario. Together, they fought their way out of St. Peter's Basilica, and climbed a tower, where Ezio prepared to drop the Apple of Eden into the Tiber. However, upon realizing his insecurity, Mario took the Apple and promised to keep it safe until Ezio could make a decision. The two then proceeded to return home to Monteriggioni.

Siege of Monteriggioni

Mario: "I am keeping it safe. The Borgia must not be allowed to breach the walls until everyone is safely away. Insieme per la vittoria!"

Ezio: "Insieme. Uncle... be careful."

―Ezio and his uncle before the siege

Ezio meeting with the other Assassins

During the journey with his uncle, Ezio told Mario what he had learned from Minerva, but also found solace in the fact that his own battles were finally at an end. That evening, Ezio once again retold the events of his encounter in the Vault, this time to Niccolò, his sister, and mother.
Niccolò in turn criticized Ezio for his failure to kill Rodrigo Borgia, and angrily left for Rome. That night, unconcerned with Niccolò's outburst, Ezio returned to his bedchamber to share an intimate night with Caterina Sforza. He soon learned that the Borgia threat was far from over.

Ezio using a cannon during the siege

On 2 January 1500, Cesare Borgia, the son of Rodrigo, Commander of the Papal armies, and a high-ranking Templar in his own right, laid siege to Monteriggioni.
Taking the Assassins by surprise, Cesare's forces were quickly able to level half the city before Ezio managed to reach the cannons above the ramparts. He and the Monteriggioni mercenaries returned fire, destroying many of Cesare's own siege weapons.
Despite knowing this to be a futile effort, they managed to stave off the attackers long enough for the citizens to reach safety. However, as Cesare's forces managed to breach the city gates, Cesare brought a mortally wounded Mario Auditore and captured Caterina Sforza before him.
Seeing his uncle lying on the ground, Ezio ran across the rooftops in a vain effort to reach them, but was shot by arquebusiers upon the city walls. At the same time, Cesare "invited" Ezio to come to Rome with a shot of his own firearm, killing Mario.

Ezio and the others escaping through the Sanctuary

Ezio, having soon regained consciousness as two of Mario's mercenaries dragged him to safety, continued to partake in the battle, which had spilled into what was left of the city streets.
Retreating to the Sanctuary, Ezio and the fleeing civilians fled through a secret passageway that had been hidden behind the statue of Altaïr Ibn-La'Ahad.
After ensuring his mother and sister were safe, Ezio began to make his way for Rome. During this journey, however, Ezio passed out and fell from his horse due to the severity of his wounds.

Moving to Rome

"There will be no peace until we rise up against the entire Borgia family and the Templars who serve them."

―Ezio discussing his motives for staying in Rome.

Margherita treating Ezio's wounds

Ezio eventually awoke to find his wound being treated by a stranger, Margherita dei Campi,^[9] who told him that he had simply been dropped off at her home by a man who wished for Ezio to meet Niccolò de Machiavelli at the Mausoleo di Augusto.
The man who had brought him there had also supplied him with a new set of Assassin robes. After leaving the house, Ezio retrieved some medicine from a local doctor, and searched for Niccolò in front of the Mauseleo.
Ezio's attention was soon caught, however, by the discussion of a group of guards who were set on injuring an innocent civilian for "causing the Borgia guards trouble". Following the guards and aiding the distressed civilian, whose wife had recently been executed by a Borgia ally known as Il Carnefice, Ezio got his first taste of life in Rome.
Making his way up to Il Carnefice's abode, Ezio assassinated him and continued on his way to meet with Niccolò. From him, Ezio discovered that Rome had fallen into a state of disrepair under the Borgia, and that its citizens were being heavily oppressed. Niccolò also told him of Cesare Borgia, the man responsible for the death of Mario Auditore.

Ezio conversing with Niccolò and Fabio

Together, Ezio and Niccolò met with Fabio Orsini, the cousin of Bartolomeo d'Alviano who had been forced into serving Cesare Borgia. Fabio lent to the Assassins an old storehouse of his on Tiber Island, in the hope that they would find a better use for it.
From here, Ezio traveled to the Rosa in Fiore in an attempt to gather the support of the city's courtesans. When he arrived however, he learned that madonna Solari, the head of the brothel, had been kidnapped by the Cento Occhi, Cesare's hired thugs, and was being held for ransom.
Gathering the funds necessary, Ezio made his way to the kidnappers' location, only to be double-crossed. Madonna Solari was killed, and the Cento Occhi attacked Ezio. Ezio survived the ambush and returned to the Rosa in Fiore to discover his mother and sister there. With no one to lead them, the courtesans turned to Claudia Auditore to act as their Madam, with a very reluctant Ezio agreeing to her appointment.
Ezio then moved on to gather the support of both La Volpe's Roman thieves, who were suffering at the hands of the Cento Occhi, and Bartolomeo's mercenaries, who were under attack by the French.

Aiding Copernicus

"If the Borgia are involved, then so am I."

―Ezio, after noticing the guards attack Copernicus.

In 1500, while passing the Campidoglio, Ezio noticed a scholar by the name of Nicolaus Copernicus giving a strange speech to the Roman citizens. After having asked another spectator about the man's identity, he learned that the man came from the Vatican, though spoke contrary to the Church's teachings.
However, Ezio soon saw a battalion of Borgia guards attack Copernicus, and swiftly stepped in to defend him. Afterwards, the two men introduced themselves to one another, with Copernicus admitting to having been a Templar himself, until he disagreed with the other Templars on keeping the findings of his scientific experiments hidden from the public.

Copernicus giving Ezio the letters

Upon hearing that more Borgia guards were looking for Copernicus, they quickly left the Campidoglio and went looking for a hideout. Evading the Borgia guards, Ezio found shelter for Copernicus in a small house in the Antico District, next to the Colosseum.
Once they were safe, Copernicus realized that his fellow scholars would be in danger as well, and asked Ezio to deliver a letter of warning to each of them. Despite being insecure on whether to trust Copernicus or not, Ezio agreed to deliver the letters.
Ezio traveled across the Centro District, handing letters to several scholars, and managing to reach most of them in time. He returned to Copernicus in the countryside, who told him that the Master of the Sacred Palace, a priest appointed by the Pope to ensure that Roman religious philosophy remained pure, was most likely the person responsible for the attacks.
Ezio followed a cardinal roaming nearby, who eventually led him to the Master. Eavesdropping on their conversation, Ezio found out that the Master had sent his best men to kill the scholars whom Ezio had delivered the letters to, and he quickly rushed to save them. Ezio successfully managed to assassinate all of the hired men, and returned to Copernicus.

Ezio and Copernicus looking at the eclipse

He informed Copernicus that his suspicions were correct, and warned him of his own safety, but Copernicus forewent caution, as he wanted to chronicle an eclipse that night. Ezio set off once again, with the intention of killing the Master.
Ezio found the Master and killed him with his Hidden Blade, and with his dying breath, the Master revealed that he had already sent his best man to kill Copernicus. Ezio quickly set off to where Copernicus would research the eclipse, and arrived just in time to kill the assassin.
As they looked up at the eclipse together, Copernicus revealed to Ezio that the sun was most likely the midpoint of the universe, contrary to common believe that it was the Earth. Copernicus thanked Ezio for his aid, and they went their separate ways.

Infiltrating the Castel Sant'Angelo

"Do not worry. The Borgia will die. You have my word."

―Ezio, after agreeing on killing Rodrigo and Cesare.

After receiving intelligence reports from Claudia, La Volpe and Bartolomeo indicating that Caterina Sforza was being held in the Castel Sant'Angelo, Ezio departed to rescue her, though not before Niccolò demanded that, given the chance, he prioritize killing Cesare and Rodrigo.

Ezio carrying Caterina

Infiltrating the stronghold in 1501, Ezio scaled the fortress' double walls and apprehended Lucrezia Borgia, who was holding the keys to Caterina's cell. From there Ezio and Caterina escaped, making sure that they remained undetected until they reached the stables.
They fled across the Ponte Sant'Angelo, and Ezio ordered Caterina to ride on as he dealt with the pursuing guards. Only a timely explosion from within the Castel prevented him from being overwhelmed.
Returning to his base of operations, Ezio decided that in order to free Rome from its Borgia oppression, he needed to involve those who were being oppressed. Despite Niccolò's protests, the two agreed to begin recruiting citizens of Rome into Ezio's new Brotherhood, so that the liberation of Rome could begin.

Expanding the Brotherhood

"I say we work here. In Roma. Erode the Borgia’s influence while restoring our own. And in fact, I want to begin right now."

―Ezio revealing his plans to fight against the Borgia.

Ezio recruiting a citizen

Within a year, Ezio had turned a number of Rome's citizens into Assassin apprentices,^[5] and had adopted several existing members of the Order into his guild, such as Francesco Vecellio, whose former master had betrayed the Order.
The apprentices fought and trained alongside Ezio, and undertook missions to aid their fellow Assassins in cities across Europe and beyond, including Calicut, India. Ezio also had his apprentices aid him in removing a number of Templar agents, such as Malfatto and Silvestro Sabbatini.
Eventually, Ezio received a surprise visit from his old friend Leonardo da Vinci, who informed him that he had been pressed into providing the Borgia with various forms of advanced weaponry and War Machines. Leonardo promised to provide Ezio with the tools necessary to destroy his weapons, albeit at a small monetary cost. Ezio agreed and managed to demolish all of Leonardo's machines in his war against the Borgia.

Finding the Banker

"If we cut off his funds, Cesare will lose his army and return without his men. So, I ask you, where does he get his money?"

―Ezio, asking the other Assassins about the Banker.

Ezio at the meeting in the hideout

Ezio met with Niccolò, La Volpe, Claudia, and Caterina in the Assassin hideout, where they discussed their plans to attack the Borgia. Ezio asked them for the source of Cesare's funds, to which La Volpe replied that Cesare had his own personal banker, whose identity was unknown, as he was only referred to as "the Banker".
Additionally, Ezio revealed that he intended to kill the French general, Octavian de Valois, so that Cesare would lose the protection of his foreign allies. La Volpe also remarked that there was a side entrance into the Castel Sant'Angelo that Ezio could use, and that Lucrezia's lover Pietro Rossi had a key to enter it.
Upon leaving the hideout, Ezio noticed Caterina about to leave on horseback; she said that she was of no good to anyone without Forlì in her possession, and that she wanted to be with her children in Florence. Despite Ezio's request for her to stay, Caterina left Rome.

Ezio handing the money to Egidio

Ezio met Claudia in the Rosa in Fiore, and she told him that senator Egidio Troche frequently came into the brothel to complain about his debts to the Banker, and that he could be found at the Campidoglio. Hearing several men on the Campidoglio talking about Egidio making failed attempts to get finances, Ezio eventually found him under attack of Borgia guards and rescued him.
Together, they went through the district looking for a safe place for Egidio to hide out in. Finally, Egidio found shelter in the home of his brother Francesco, who was angry at Egidio for warning the ambassador of Venice of Cesare's plans for Romagna.
Egidio was willing to aid Ezio, telling him that the Borgia guards usually led him to the Banker, and that he needed money to meet with them. Ezio brought him the required amount of florins, and Egidio met with the guards, while Ezio followed them from above.

Disguised Ezio handing over the chest

Eventually they arrived at the Pantheon, where the money was given to the Borgia captain Luigi Torcelli. Ezio infiltrated the Pantheon via the roof and killed Luigi, taking his clothes and impersonating him. Together with two Borgia guards, Ezio was able to carry the money to the right location - a feast Cesare was throwing in celebration of his conquests - and passed the chest of money on to the next guard.
Ezio was given entry to the party, but the guards soon found out that Luigi had been killed in the Pantheon, and they went out looking for Ezio. However, with the aid of Claudia's courtesans, he was able to remain undetected while following the chest carrier to the party.
Once there, Ezio overheard the Banker introduce himself as Juan Borgia to a courtesan. Ezio followed them both to where Cesare was giving a speech. Ezio avoided the patrolling guards and took a seat on a bench, killing Juan Borgia as he passed him.
Ezio escaped and returned to the Rosa in Fiore, where a group of courtesans who had stolen the chest of money cried out that the Borgia guards had followed them to the brothel, and that they had gone after Claudia and Maria. Ezio rushed inside, only to find out that Claudia had already killed all the Borgia guards by herself using a knife.

Battle with the French

Ezio: "Once inside, your men can overpower the camp's patrols, correct?"

Bartolomeo: "Yes, but..."

Ezio: "Especially if the patrols are taken completely by surprise?"

—Ezio and Bartolomeo forming a plan

Disguised Ezio delivering Bartolomeo to Octavian

Following the Banker's death, Ezio traveled to Bartolomeo d'Alviano's barracks, where he soon discovered that Bartolomeo's wife, Pantasilea Baglioni, had been kidnapped by the Baron de Valois, commander of Cesare's French allies in Rome. Despite putting up a valiant defense of his barracks, Bartolomeo saw no feasible way that he could secure his wife's safety short of surrendering; Ezio however, had another idea.
After Ezio eliminated a large number of French soldiers, Bartolomeo's mercenaries wore their armor and took on the guise of a French patrol escorting a defeated Bartolomeo to the Castra Praetoria, the base of operations for the Baron de Valois' forces.
Infiltrating the fortress, Bartolomeo and Ezio came face to face with the Baron, who very nearly killed Pantasilea, had not Ezio interrupted him with a shot from his Hidden Gun. Battle soon broke out, and with Bartolomeo's mercenaries engaging the French forces, Ezio was free to pursue the Baron and Pantasilea, eventually freeing her and killing him.

Securing the keys to the Castel

"It is time to pay a visit to Lucrezia's lover, Pietro."

―Ezio on obtaining the key to the Castel.

Not long after his victory over the Baron de Valois, Ezio traveled once more to La Volpe Addormentata, where he and La Volpe discussed the latter's suspicion that Niccolò had betrayed the Assassins by guiding the Papal Army to Monteriggioni, and by informing Rodrigo and Cesare to stay away from the Castel during Ezio's infiltration. Ezio disagreed, but promised to look into the presence of a traitor.
La Volpe informed Ezio that Pietro Rossi, an actor and Lucrezia Borgia's lover, had the key to the Castel and that Cesare intended to kill Pietro over his feelings for Lucrezia. Locating Cesare at one of the city gates, Ezio witnessed the assassination of Francesco Troche, brother of Egidio, by Cesare's personal assassin Micheletto Corella.
Ezio then tailed Micheletto, who was to infiltrate the play that Pietro would appear in, and kill him. As he followed him, Ezio had his apprentices discreetly replace the guards Micheletto tasked with partaking in the murder.

Ezio apprehending Paganino

Eventually, Micheletto arrived at the site of the play, the Colosseum. Climbing up the outside of the structure, Ezio made his way down from the roof to the backstage area below, picking off Micheletto's marksmen as he went. Ezio soon struck Micheletto, but spared his life when he learned that Pietro had been poisoned previously, as a means of insurance.
Ezio hurried from the Colosseum with Pietro in his arms, while his apprentices covered the retreat. After handing Pietro over to a doctor and receiving the key to the Castel from him, Ezio spotted Paganino, a member of the Venetian thieves guild who had been present at the siege of Monteriggioni.
When approached, Paganino ran and Ezio gave chase. Ezio quickly caught him and reasoned that he was in fact the traitor, not Niccolò. Paganino pressed Ezio's Hidden Blade into his own throat to kill himself rather than risk further revelations. Ezio raced back to Tiber Island to stop La Volpe from killing Niccolò.

Ezio being promoted to Mentor

Later meeting with La Volpe inside the Tiber Island hideout, Ezio ordered him to gather the Assassins, and bring Claudia as well. They gathered in the ceremony hall, and there Ezio offered Claudia a chance to join the Order, just as the others of their family had. She agreed, and was inducted into the Order.
At the time, Niccolò also decided to step down from leading the Order, and to promote Ezio to the position of Mentor, realizing that Ezio was both a better leader, and "exactly what the Order needed". Ezio in turn appointed Niccolò as his trusted adviser, who then recommended he finish what he started. Ezio consented, and left for the Castel Sant'Angelo.

Fall of the Borgia

Ezio: "You'd better not stop telling me what you think. Why else would I seek the opinion of my most trusted advisor?"

Niccolò: "Go kill them, Mentore. Finish what you started."

Ezio: "Good advice."

—Ezio and Niccolò discussing the Borgia.

Ezio giving Rodrigo last rites

With Cesare's supporters in Rome dead, the Brotherhood and its allies were in command of the city. Ezio was informed that Cesare had returned to Rome, and was meeting with his father in the Castel Sant'Angelo. Once again infiltrating the Castel, Ezio witnessed Rodrigo's attempt to poison his son, only to be murdered in retaliation.
As Cesare hurried off to obtain the Apple of Eden that his father had hidden away, Ezio entered the Castel and gave Rodrigo's body his blessing. He then learned from Lucrezia where Rodrigo had hidden the Apple, and raced out of the fortress.

The Assassins making their final stand against Cesare

Ezio arrived at St. Peter's Basilica, and took possession of the Apple before Cesare, with just moments to spare. Cesare arrived with a sizable contingent of Papal soldiers, though Ezio managed to escape them. Over the next few months, and with the help of his fellow Assassins, Ezio used the Apple to completely destroy what little support Cesare still had in Rome.
Eventually, the Assassins caught up with Cesare himself, who was awaiting reinforcements from Micheletto and his army by the gates of Rome. Cesare's forces were defeated, although their leader had retreated behind the city portcullis. However, he soon realized that he was not safe as he was quickly arrested by Fabio Orsini on the orders of Pope Julius II. As he was dragged away, Cesare screamed that chains would not hold him, and that no man could murder him.

Ezio and Leonardo looking into the Apple

Despite their victory, Ezio was troubled by Cesare's comments, and upon meeting with Leonardo, he confessed his concerns. At Leonardo's suggestion, Ezio decided to look into the Apple to see if Cesare's threats were true.
Upon doing so, Ezio quickly let go of the Apple, standing before Leonardo could question him and commenting that he had to leave immediately. Before he departed, however, Ezio left Leonardo a parting gift: a chest full of gold, in compensation for losing his patron.