- "It's finished, Rodrigo! Lay down your arms, and I'll make sure the end comes swiftly."
- ―Ezio to Rodrigo during their confrontation, 1499.[src]
Upon learning of this development, members of the Italian Brotherhood prepared themselves to fight through strong opposition and assassinate Ezio's foe Rodrigo Borgia within the Vatican to gain access into the fabled Vault.
Dealing with the Templars responsible for the death of his father and brothers, Ezio assassinated Rodrigo's allies scattered across Italy, taking his quest through Florence, Tuscany, Forlì, Venice, and even Spain.
With the death of all his followers, only the Grand Master himself remained. Ezio journeyed to the Vatican to avenge the deaths of his father and brothers, confront Rodrigo and discover the secrets of the Vault.
- Ezio: "It is time, uncle. Let us finish what you and my father started all those years ago..."
- Mario: "Indeed. Perhaps now we can finally make sense of this prophecy - and put a stop to whatever it is the Spaniard is plotting."
- ―Mario to Ezio before revealing the Codex's secrets.[src]
After collecting all of the Codex pages, the Order met in Mario Auditore's study room in the Villa Auditore at the Assassin's stronghold, Monteriggioni. There, Ezio inspected the Codex pages that were placed on the wall to discover the message hidden beneath them.
Marveling, Ezio stated that some of the landmasses depicted on the map did not exist, though Niccolò Machiavelli corrected him that they possibly did, or were simply yet to be discovered or rediscovered over time.
To Ezio's shock, he saw that the Vault was located roughly right where the city of Rome stood. It was then that he theorized that Rodrigo Borgia had become Pope in order to receive possession of the Papal Staff, and to gain access to the Vault.
When Teodora questioned Ezio's meaning, Mario explained the prophecy from the Codex, stating that two Pieces of Eden in conjunction were necessary to open the Vault; one of the Apples, and the Staff. The other Assassins began to speculate about what the Vault would contain, and expressed their fears of what Rodrigo would do once he had attained it.
Ezio decided that he would confront Rodrigo and try to open the Vault himself. The other Assassins agreed, offering to "cause trouble in the city" to keep the Borgia guards from stopping or interfering with Ezio's mission. With his mission planned, and his final vengeance in sight, Ezio departed for Rome that December.
Ezio arrived in Rome outside the Castel Sant'Angelo, and began to scale the building until he had climbed onto the Passetto di Borgo. Stealthily killing off the patrolling guards and mounting a horse, he was able to rapidly cross the wall and eliminate any opposing troops on it, finally reaching an entry point into the Sistine Chapel.
Ezio blended with the monks and cardinals, in order to keep the guards from detecting his presence. Traversing beams, ropes, and other constructions high above the ground, Ezio made his way within striking range of the Pope as he led the Mass, leaping at him from above and hitting Rodrigo with some force, seemingly knocking him unconscious.
- "I thought... I thought I was beyond this. But I'm not. I've waited too long... lost too much... Requiescat in pace, you bastard!"
- ―Ezio's first assassination attempt on Rodrigo Borgia.[src]
Holding Rodrigo at his mercy, Ezio allowed his anger and hatred for him to overwhelm him, remembering Rodrigo's part in his family's destruction. However, as he prepared to deal the final blow, Rodrigo reawakened, and smashed Ezio aside with the Staff.
Before anyone in the Chapel could react, Rodrigo used the Staff's powers to drain the life energy from the assembled priests and guards to heal and energize himself; only Ezio, protected by the Apple's power, was immune to the effect.
Rodrigo demanded that Ezio hand the Apple over to him, but the Assassin dared the Pope to take it from him. He then used the Apple's power to produce four illusions of himself.
Ezio and Rodrigo then engaged in a brief duel, until Ezio finally managed to wear him down, forcing the Pope to collapse from exhaustion. Ezio demanded that he stand down and accept his offer of a quick death, but Rodrigo, asking if Ezio would give up so easily if their positions were reversed, again went on the offensive.
Again Rodrigo made use of the Staff's power, blasting Ezio off his feet and making himself invisible. As Ezio struggled to recover, Rodrigo seized the Apple from him and combined it with the Staff, magnifying its powers greatly. With that, Rodrigo used the Staff to lift Ezio up and suspend him in midair.
As the Assassin dangled helplessly, Rodrigo stabbed him in the abdomen with a knife and ended the Staff's hold, dropping the injured Ezio to the floor. Just before he passed out, Ezio saw Rodrigo descend down a hidden staircase in the Capella's floor.
The Vault's atrium
- "It's over, Rodrigo. No more tricks. No more ancient artifacts. No more weapons. Let us see what you are made of, old man."
- ―Ezio challenges Rodrigo Borgia to a final fight.[src]
Some time later, Ezio regained consciousness. His wounds were not fatal due to his armor blunting the attack, thus he got back to his feet and investigated the altar that he had seen Rodrigo disappear into.
Finding the hidden doorway, Ezio followed the Pope down the staircase into a strange underground corridor until he came to a large, open chamber below him; the atrium of the Vault.
There, he could see Rodrigo desperately trying to open the Vault's door. Ezio dropped down and, casting aside his sword, short blade, and hidden gun, challenged Rodrigo to one last fight, free of trickery, ancient artifacts, or weapons. Rodrigo reluctantly accepted, and the pair brawled using only their bare fists.
As they fought, Ezio demanded to know what lay within the Vault that the Templars wanted so badly. Rodrigo displayed surprise at the fact that the Assassins were unaware of the truth, and claimed that God was what lay inside. Ezio was somewhat skeptical at this declaration, and asked what Rodrigo intended to do with this knowledge. Rodrigo replied that he intended to release God and seize his power, a feat made possible through the combination of the Staff and Apple.
Ezio remarked that he doubted a couple of ancient relics could harm a god, but Rodrigo sneered that he knew nothing, that his images and views on God were taken from a book written by men.
When Ezio challenged Rodrigo for dismissing Christianity's central text, Rodrigo laughed, saying he had only become Pope to gain access to the Vault and the power such a position granted. He claimed not to believe a single word of the Bible, deriding it and every other religious text as superstitious lies.
- "No. Killing you won't bring my family back. I'm done. Nulla è reale, tutto è lecito. Requiescat in Pace (Nothing is true, everything is permitted. Rest in Peace)"
- ―Ezio, sparing the life of Rodrigo.[src]
After a lengthy fight, Ezio gained the upper hand and seized Rodrigo by the throat. He throttled his old enemy into submission and finally held him at blade point.
Astounded, Rodrigo yelled that Ezio could not open the Vault, as it was his destiny as the Prophet to open it. However, Ezio revealed the truth to Rodrigo, announcing that he was not the Prophet, nor had he ever been.
Broken and humiliated by this revelation, Rodrigo told Ezio to kill him and be done with it, but Ezio refused to kill for the sake of vengeance and relinquished his long-felt hatred and desire for Rodrigo's death. Ezio simply acknowledged that killing Rodrigo would not bring back those he had loved and lost.
Leaving his defeated nemesis on the floor, Ezio remarked how he had been beaten - because "nothing is true, everything is permitted" - and paid him no more heed. Turning to the Vault, Ezio used the combined power of the Staff and Apple to open the chamber directly in front of him, and then entered to discover its secrets.
- "We were strong- but you were many, and both of us craved war. So busy were we with earthly concerns, we failed to notice the heavens... and by the time we did, the world burned until naught remained but ash."
- ―Minerva trying to explaining to Ezio what had happened to her race.[src]
Entering the Vault, Ezio was confronted by a holographic image of Minerva . After confirming that he was the Prophet by showing the figure the Apple, the woman declared that they must speak, though she seemed to not be speaking directly to him.
Astounded, Ezio theorized that they were gods. Minerva laughed at this, saying that she and her kind were not gods, but had simply come before. She explained that humanity had not understood them when they existed, but while they could not comprehend her, they would comprehend her warning.
Ezio stated that her words made no sense to him, but Minerva replied they were not meant for him, confusing Ezio further as no one else was present. Minerva proclaimed that she was not communicating with Ezio, but through him; thus his part in all this was finished.
She explained that Ezio was an anchor for the one she wished to communicate with, and politely asked him to be silent to assist her mission. Ezio listened as she delivered a confusing warning of an impending celestial disaster to an individual called Desmond and a history of the relationship between her people and humans before fading away.
As she departed, Ezio begged her to wait, since he still had so much to ask, but she vanished without another word, leaving Ezio's questions unanswered.
Reunited with Mario
- Mario: "Did Rodrigo manage to hurt you?"
- Ezio: "Barely, my armor blunted his attack."
- ―Mario and Ezio talking while escaping Rome.[src]
Once Ezio made the discovery of the Vault, he emerged from the main chamber to find Rodrigo gone, only his Pope garb remaining. Ezio then inspected the Staff and attempted to pull it out of the ground; though this proved futile as the Staff descended into the ground, and was sealed beneath the Vatican.
After its disappearance, the floor Ezio stood on also sank lower. Mario then appeared above Ezio, reassuring him that the Staff was "better in the hands of the earth than the hands of man", before instructing him to climb up so they could leave. After rejoining his uncle, Ezio told Mario of what he had seen and the questions that needed answering, but Mario told him to speak of it later.
The Apple's fate
- "This decision is yours alone to make. Only do so quickly."
- ―Mario to Ezio about the Apple's fate.[src]
As the two made their escape, they were attacked by guards. Though Ezio and Mario easily overpowered them and escaped into the Vaticano district.
Ezio, however, could not bring himself to get rid of an artifact of such power, thus Mario assured him that he would take care of the Apple until Ezio made his decision. Afterwards, they both returned to Monteriggioni.
- "Better in the hands of the earth than in the hands of man. "
- ―Mario to Ezio after the Staff descended down into the ground.[src]
Succeeding in opening the Vault, and preventing the Templars from obtaining its contents, the Assassins withdrew from Rome and Ezio retired to Monteriggioni, hoping to recover from his trials.