Chasing Cesare

Captain: "Cesare’s escaped!"

Ezio: "When?"

Captain: "The guards were being changed. About half an hour ago."

—Ezio discovering Cesare's escape

Running from the Tiber Island headquarters, Ezio made his way to the Castel Sant'Angelo and was greeted by a scene of mass confusion. Questioning a guard, Ezio learned that Cesare had escaped, likely with the aid of an inside-man, but that Lucrezia had been left behind. Concluding that the best way for Cesare to escape the city was by boat, Ezio ran to the docks nearest the Castel.
The docks were extremely busy when he arrived, and as such, Ezio was forced to use the Apple to learn of Cesare's location. Pointed to a red-sailed caravel on pier six, Ezio made his way there, only to find that it had already set sail. Ezio headed to the nearest boat and offered to pay the boat-master handsomely if he pursued the caravel. Ezio was surprised to see that it was Claudio who captained the boat, having been given money to do so by La Volpe previously.
The ships were already nearing Ostia by the time Claudio's scoop caught up. Locking sails, Claudio gave Ezio the order to jump aboard and together Ezio and Claudio quickly overpowered the ship's crew, while Cesare watched helplessly from the secure wooden crate he had been hidden in. Upon docking in Ostia, Cesare was securely sent back to Rome.

Councilor to the Pope

Julius II: "Cesare Borgia has been safely delivered into one of their strongest and most secure rocca!"

Ezio: "Where?"

Julius II: "Ah, that's classified information, even to you. I can't take any chances with Cesare."

—Pope Julius II speaking with Ezio.

By 1504, Ezio had become councilor to Pope Julius II, and was with him when the Pope received word that Cesare Borgia had been successfully handed over to King Ferdinand II of Aragon, and his wife Queen Isabella I of Castile. When Ezio inquired as to where he was being held, Julius politely refused to answer, perhaps cautious of any attempts Ezio might make on the Templar leader's life. Later in the conversation, a tired Ezio nonchalantly suggested the name "Swiss Guard" for the contingent of Swiss mercenaries Julius II was thinking of hiring as his personal bodyguards.^[9]
The following day, Ezio called a meeting with La Volpe, Bartolomeo, Niccolò, and Claudia to discuss rooting out the Borgia diehards who still pocketed Italy. Together, they formulated a plan that would keep control of the Borgia loyalists until the time to strike presented itself.
Following the meeting, Ezio and Niccolò met with a number of Rodrigo's former lovers and associates, including Vannozza dei Cattanei and Giulia Farnese, as well as Cesare's wife, Charlotte d'Albret. On their way to meet Giulia, Ezio and Niccolò noticed they were being followed by someone, and had been since leaving Vanozza's palazzo. After making their way onto the rooftops, the Assassins were eventually able to lose their pursuer, although it took a lot of effort on their part.
During this mission, Niccolò repeatedly asked Ezio to use the Apple to more easily locate Cesare; Ezio consistently refused, not wishing to become dependent on its power at the expense of his own skill and experiences.

Dealing with the Borgia diehards

Bruno: "The Borgia diehards! They sent someone to follow you and Maestro Ezio-"

Niccolò: "And?"

Bruno: "Sure that you were out of the way, they have taken Claudia!"

—Ezio and Niccolò discovering Claudia's capture.

After leaving Charlotte's palazzo, Ezio and Niccolò were approached by Bruno, one of Niccolò's spies, who informed the two that the Borgia had had them followed, so as to ensure they were not present when they kidnapped Claudia Auditore. Upon learning her location, the two quickly made their way to liberate her from her captors, only to discover they had been led into a trap; Bruno had been working for the Borgia for at least a year.
Upon reaching the Borgia diehards' facility, Ezio saw Claudia tied to a chair, half-dressed and bruised. The leader of the diehards held a knife to Claudia's throat and threatened to kill her if Ezio did not leave Rome once and for all. Ezio refused and, together with Niccolò, quickly overpowered and eliminated the diehards.
After rescuing Claudia, Ezio learned that Micheletto had holed up in the Ludus Magnus in Zagarolo, east of Rome. Bringing together a force of one-hundred apprentices and thieves, Ezio's forces quickly surrounded and overpowered the two-hundred and fifty strong force commanded by Micheletto.
Micheletto was taken to Florence, and was incarcerated in the cell atop the Palazzo della Signoria; the same cell that had held Ezio's father twenty-eight years earlier. There, he was tortured by Niccolò, Amerigo Vespucci and Piero Soderini, the Gonfaloniere of Florence and Niccolò's "master". Despite learning nothing from Micheletto, Niccolò promised to continue in his attempts to prise any information from him, and parted ways with Ezio warmly when the latter was forced to return to Rome.

Locking away the Apple

"I have more than played my part in your career and you must now return me."

―The Apple to Ezio.

Days later, Ezio was awoken in the early hours of the morning by Niccolò, who informed him that Micheletto had managed to escape from the Palazzo della Signoria with the aid of a Borgia-friendly priest and the diehards. Ezio quickly realized that this could work to their advantage: if they could track Micheletto down, they could follow him to Cesare.
Convening an emergency meeting, Ezio organized a manhunt for Micheletto that focused on the area surrounding Rome and Ostia. Later, Ezio was effectively ordered by Niccolò to use the Apple to locate Micheletto, but was only provided with a vague image of a Spanish castle.

Ezio walking out of the Vault

Ezio was confused by this, and expressed his feelings to Niccolò, who recommended he ask the Apple why it wasn't showing him what he wanted. The Piece of Eden told Ezio that the time had come for him to relinquish it, so that future generations might make use of it, and also indicated where it should be hidden. As a parting gift, the Apple informed the Assassin that Micheletto was making his way to Spain via the port in Naples.
Before making their way to Naples, Ezio and Niccolò decided to abandon the Apple just at it had requested. Entering the Colosseum, the two Assassins made their way through the old lair of Romulus, marking the way as they went, until they reached the entrance to the Vault.
Ezio entered the Vault, placed the Apple on the central pedestal, and exited. As the door closed behind him, both Ezio and Niccolò noticed that the door seemed to vanish, instead taking the appearance of the surrounding wall.

Rescuing Da Vinci

Leonardo: "Salaì? Is that you? Ezio! I must be getting lazy in my old age. I did not know you had returned to Roma."

Ezio: "Unfortunately, I cannot stay. I am here to charter a ship."

―Leonardo and Ezio, shortly after the latter's return.

Ezio and Leonardo looking at the unfinished Mona Lisa

With the Apple safely hidden away, Ezio met with Leonardo in 1506 to discuss his need of chartering a ship to Navarre. Leonardo interjected that he knew the name of a friendly ship captain, but was unable to remember it at the time. As the artist searched for his records, Ezio and Leonardo briefly discussed the ancient Greek scholar Pythagoras, whom Leonardo was researching.
However, Ezio suggested he instead focus on his painting, and complimented a portrait of a smiling lady Leonardo was working on. Eventually, though he could not find the captain's name, Leonardo offered to accompany Ezio to the docks, though he was unable to leave the studio unaccompanied. As such, Ezio offered to bring back Leonardo's apprentice, Salaì.

Ezio meeting Salaì in La Volpe Addormentata

Ezio found Salaì in La Volpe Addormentata, enjoying a game of dice. Despite some initial resistance, Salaì eventually agreed to return to his Master's workshop with Ezio, much to the chagrin of three cloaked individuals who had been playing against Salaì.
Once outside, the three individuals and several of their comrades, who were all revealed to be Hermeticists, attacked Ezio and Salaì. The two manage to defeat them, and Salaì remarked that only one individual could fight with such skill, correctly guessing Ezio's name. Ezio simply suggested that they continue on to Leonardo's workshop.
Avoiding the throngs of Hermeticists between them and their destination, Ezio and Salaì returned to find the workshop wrecked and Leonardo missing. Salaì regretfully informed Ezio that he did not know the location of the Temple of Pythagoras, which was likely where Leonardo had been taken.
Looking down to the floor in sadness, Salaì spotted some writing on the floor, which suggested that Leonardo's artwork that had hung in the Villa Auditore had held clues to the location of the temple. At first Ezio was dismissive, commenting that all the paintings had been destroyed in the attack, though Salaì quickly responded that only two had been destroyed, and one had been sold (by Salaì himself to buy a "now out of fashion" doublet), leaving five more to find. These five, he said, were currently in the hands of Lucrezia Borgia, Duchess of Ferrara.

Recovering the paintings

"I count five Leonardo da Vinci paintings you have stolen, and I want them returned."

―Ezio to Lucrezia, Duchess of Ferrara.

Ezio seducing Lucrezia inside Delizia di Belriguardo

Ezio made his way to Delizia di Belriguardo, climbing over the palazzo's outer walls and overhearing a paranoid Lucrezia ordering the guards into high alert. Infiltrating the palazzo through the attached stables, Ezio confronted Lucrezia on the stolen paintings, clarifying that he had not come to take her life.
Willingly, Lucrezia revealed that she only had one of the paintings left, as the rest had been taken after the fall of her family. Ordering her men to place the Annunciation painting in a cart outside the palazzo's walls, Lucrezia was then thrust against the wall by Ezio, who began to kiss her neck intimately.
At this, Lucrezia told Ezio that three of the paintings had been sold to Francesco Colonna, while the fifth went to an old flame of Lucrezia's named Patrizio. Ezio apologized to Lucrezia and then pulled back, revealing that he had tied her to the hanging drape. Lucrezia angrily called for her husband's personal guard, who pursued Ezio through the palazzo until he escaped out of a window, and into a bale of hay near the cart containing the painting.
Returning to Rome, Ezio made his way to the Vaticano district, where he followed Patrizio, who was hoping to sell Portrait of a Musician to the Hermeticists. Ezio watched as Ercole Massimo belittled Patrizio for his racist views on Lucrezia's Spanish heritage, and then had him murdered when he tried to destroy the painting out of anger. Ezio pursued the Hermeticist Ercole had tasked with transporting the painting, and eventually retrieved it.

Ezio interrogating Duccio

Ezio then traveled to the home of Francesco Colonna, only to find that the house had been seized by the bank. He was told that the da Vinci paintings had been sold to an art merchant from Florence, who was waiting at the docks outside the Mausoleo di Augusto.
Making his way there, Ezio was surprised to see that the art merchant was his sister's former love interest Duccio de Luca. Duccio immediately set about insulting Ezio for living in a "third-rate city" such as Rome, and then again for his sister being the Madame of the Rosa in Fiore. For his troubles, Duccio received a short, stout punch to the face from a now angered Ezio.
Duccio ordered his entourage to attack Ezio, though the Assassin was able to easily hold off his attackers. He eventually gained the information he wanted from Duccio, but the merchant pushed his insults even further against Claudia, resulting in a final blow, which knocked him unconscious.^[12]
After knocking Duccio out, Ezio made his way to the merchant's boat, which had been occupied by Hermeticists, to retrieve the third painting. Ezio swiftly eliminated them without being seen, and claimed the painting as his own. He then made his way to the Rosa in Fiore in order to ascertain a means of obtaining the last two paintings, which had been bought by a cardinal and put on display inside the Castel Sant'Angelo.

Infiltrating the art exhibition

"There is a viewing at the Castel Sant'Angelo later today. You will need an invitation. Fortunately, I know where you can procure one."

―Claudia helping Ezio.

Ezio entering the art exhibition

Upon reaching the Rosa in Fiore, Ezio spoke of the art exhibition with his sister Claudia, who directed him to the docks, from where one invitation was meant to be delivered. Ezio intercepted the courier carrying the invitation, and met up with a group of courtesans on the Ponte Sant'Angelo, instructing them to steal the paintings he would mark.
Ezio marked the frame of the first painting, St Jerome in the Wilderness, after distracting the guards on duty, then proceeded into the Castel for the second, backtracking along the same path he had used to escape with Caterina years previously. After marking the second painting, Adoration of the Magi, in the upper chambers, he quickly left the Castel as cries over the theft rang out around him.

Ezio and Salaì looking at the map leading to the Pythagorean temple

Ezio returned to Leonardo's workshop, where the five paintings had been stored. Inside, he found Salaì already working to find any clues for the location of the temple, though he had found nothing. Salaì was on the verge of giving up, when Ezio prompted him to think of ways Leonardo might have concealed his work. Salaì remembered that Leonardo taken to working with invisible inks, and suggested that Ezio he use his gift of Eagle Vision to find any clues. Despite his annoyance at Leonardo for telling Salaì about his gift, Ezio did as was asked, and found small diagrams in each painting.
After inspecting all the paintings, Ezio drew out each diagram and laid them on the table. Salaì immediately worked out it was a map, although there were probably pieces missing from the two paintings destroyed during the Siege of Monteriggioni. Nonetheless, Ezio managed the piece together the map, and located the entrance to the catacombs containing the Temple of Pythagoras.^[12]

Temple of Pythagoras

Leonardo: "Those are not Pythagorean symbols. 43 39 19 N 75 27 42 W. Nothing. The Cult of Hermes is wrong, the number is meaningless."

Ezio: "It is not intended for us."

―Leonardo and Ezio in the Pythagorean Vault.

Ezio and Leonardo exploring the catacombs

Ezio entered the catacombs and made his way towards the temple. As he did so, he could hear Ercole Massimo beating Leonardo, demanding he open the door to the temple. Ezio ordered the Hermeticist to stop, and after a brief exchange of words, he was attacked by Ercole's allies. He dealt with them swiftly, before climbing up to Ercole and assassinating him with his Hidden Blade.
Though Ezio suggested that they leave as Leonardo was injured, the other protested, saying that the "number" the Hermeticists had been seeking must be destroyed, lest another go searching for it. Reluctantly, Ezio agreed.
In each room of the temple, Ezio and Leonardo found themselves confronted by a complex puzzle. The first room required Ezio to redirect beams of light, while the second had him redirect the flow of air into a large, fan-dominated, locking mechanism. In the final room, Ezio had to activate several switches, which directed streams of burning oil into a central plate. Once activated, the central plate lowered, revealing a large circular pedestal.
Ezio and Leonardo recognized the symbols upon the pedestal as those shown to them by the Apple, albeit in the wrong order. Ezio watched as Leonardo rotated the pillars so the images fit, opening the door into the temple's final chamber.

Ezio and Leonardo in the Vault

Entering the vault, Ezio recognized the architecture as matching that of the Vatican and Colosseum Vaults. He approached the central pedestal and placed his hand above it. A bright light activated above him and soon enough, the entire chamber was cloaked in a dim green light. Before them, six numbers and two letters repeated themselves: 43 39 19 N 75 27 42 W.
Although Leonardo totally dismissed the numbers as nonsense, Ezio remarked that the numbers were not meant for their eyes. To distract him from the numbers, Ezio asked Leonardo of his other projects as he led him from the room.

Finishing the Borgia

Travelling to Spain

Ezio: "Where is he now?"

Captain: "Gone! I know he was in the town, asking questions, but he’s well-known here, and he has many friends, believe it or not."

―Ezio and the captain discussing Michelleto's whereabouts.

Arriving in Naples on Midsummers Day, 1506, Ezio, Leonardo and Niccolò were met with a wall of silence from the local population when they questioned them about Micheletto. They persevered, fortunately happening upon a courtesan named Camilla, who claimed to have spent the previous night with a man matching their description of Micheletto. She pointed them to the docks and to Valencia.^[9]
Ezio, Niccolò, and Leonardo booked passage to Valencia, though the crossing took five days, as the sea was particularly rough, which lost the three any chance of catching up with Micheletto. Once they arrived however, they quickly learned that Micheletto had headed to the Lone Wolf Inn, a place being described as "not for gentlemen".
Nonetheless, the three made their way to the inn and entered, only to be immediately set upon by ten men whose eyes were already accustomed to the darkness. Ezio and Niccolò fought off the ambushers, as Leonardo hid behind the bar. Ezio was then approached from behind and garroted by Micheletto himself, though a well placed strike to the stomach from Niccolò's blade forced Micheletto to let go and flee.
Although Micheletto had fled, one of his underlings had survived the Assassins' onslaught, and reluctantly surrendered his master's destination: the Castillo de la Mota. The next day, after a short rest, the three continued on to the Castillo.
They arrived too late though, and Ezio learned from a lieutenant that Cesare had escaped, although they were not yet sure how exactly he had managed it. Ezio immediately demanded a fresh horse, but Leonardo's exhaustion and Niccolò's counsel convinced him to stay a while and rest.
Within the month, they were back in Valencia, and found the city in the grip of Cesare's diehards. Disheartened by the turn of events, the Assassins contemplated their next move. Leonardo piped up with a suggestion, asking them to gather sulphur, charcoal and potassium nitrate, as well as thin sheets of malleable steel.
They complied, and in a short time, Leonardo managed to construct twenty small, hand-held bombs, which could be thrown onto enemy positions after lighting the fuse. Leonardo then revealed to Ezio and Niccolò that he was returning to Italy on the next ship, as he was becoming homesick.

Attack on Valencia

"Well, we don’t need the Apple to tell us what our old friend Cesare is planning."

―Niccolò, on Cesare's plans.

Despite this setback, Ezio and Niccolò were determined to destroy Cesare's new army, and together formulated a plan. While Niccolò made his way to the diehards' camp, Ezio headed to the docks. Approaching the first ship, Ezio lit the fuse and threw it into the vessel, dismissive of what destructive power such a small device could possible contain. He was shocked when the device exploded, cracking the warship's mast and felling it, with splintered wood flying high into the air.
Ezio continued to target Cesare's vessels, and in several cases, the initial bomb's explosion was followed by the detonation of the vessel gunpowder reserve; at one point, the explosion of one ship brought down the two on either side of it. All in all, Ezio managed to destroy twelve vessels with his ten hand-held bombs. He then met up with Niccolò on the corner of the street where the Lone Wolf Inn was located.
Climbing onto the roof of the building, Ezio and Niccolò peered over the open skylight onto Cesare and Micheletto, who were discussing the recent turn of events. Cesare angrily belittled Micheletto, blaming him for what had happened and driving him to launch himself across the table at his Master.
Cesare quickly pulled one of his pistols from his belt and shot at Micheletto, destroying his face completely. Ezio pulled back, hoping to catch Cesare as he left the building, though Niccolò, who had craned forward to get a better look, kicked down a tile in the process, and caught Cesare's attention. Drawing his second pistol just as rapidly as he had his first, Cesare shot at the Assassin, hitting Niccolò in the shoulder
Ezio briefly thought of pursuit, but Niccolò's injury was severe and required immediate medical attention. Finding a doctor, they learned the bullet had gone straight through, and that Niccolò would be sufficiently healed for travel in two weeks. Before Ezio left to pursue Cesare, Niccolò wished him good luck.

Siege of Viana

Cesare: "How did you find me?"

Ezio Auditore: "The Apple you stole from Mario Auditore led me here."

―Cesare Borgia and Ezio Auditore

In 1507, Ezio finally located Cesare Borgia, who was leading the forces of his brother-in-law, John III of Navarre, in a siege of the city of Viana.

Ezio fighting Cesare in Viana

Ezio engaged Cesare on the battlefield, initially making an unsuccessful attempt to kill him with his Hidden Blade. Cesare made his escape towards Viana Castle, and Ezio was almost overwhelmed by Cesare's guards. Narrowly surviving an artillery strike, Ezio chased after Cesare, and followed him through the village.
Fighting past the battling guards, and climbing two burning siege towers, Ezio eventually reached the ramparts of Viana Castle. He made his way through another small group of guards, and engaged Cesare in combat atop the city walls.

Ezio letting Cesare fall to his death

Despite a continual stream of soldiers attacking him, Ezio was able to whittle away Cesare's armor and overpower him. When Cesare angrily repeated his claim that no man could kill him, Ezio coldly replied he would leave him in the hands of Fate, and threw Cesare from the city walls to his death.
Later, a much older Ezio returned to the Sanctuary beneath the Villa Auditore to leave a clue to the password that protected the Vault's entrance, as suggested by Leonardo years previously. The clue was visible only to those who possessed Eagle Vision.

Search for the Masyaf Keys

Discovering a new purpose

"There, over two centuries ago, our then Mentor, Altaïr Ibn-La'Ahad, greatest of our Order, established a library deep beneath the fortress."

―Excerpt from the letter of Giovanni Auditore.

With Cesare's death, the Borgia and their plans for Italy were finished. Ezio focused himself on internal matters, forming stronger ways of communication for the Assassins from Sicily to Venice, and creating more standard training methods for new Assassin recruits.
In 1509, Ezio happened upon some of his uncle Mario's documents, finding a letter written by his father Giovanni a year before Ezio was born, which mentioned a sealed library beneath the old Assassin fortress of Masyaf; the home of Altaïr Ibn-La'Ahad, who had been Ezio's spiritual mentor during his early years as an Assassin. Driven by a will to find out more about the Order, Ezio decided to leave Italy in 1510 and set sail for Syria.

Pilgrimage to Masyaf

"None of you leave until the Assassin is dead. Do you understand?"

―Leandros sending his men after Ezio.

In May 1510, Ezio set out from Rome on horseback, accompanied by Bartolomeo d'Alviano and fifteen of the general's mercenaries. After fifteen days, they arrived at Bari, on the eastern coast of Italy. At Bari, Ezio chartered a ship, a freighter called the Anaan, and set sail for Corfu, located between Bari and Athens.
Along the way, the freighter was attacked by pirates, as it was carrying a valuable cargo of spices. Ezio joined the crew in fighting off the pirates, and assisted in capturing the pirates' captain, a man Ezio would later come to know as Al-Scarab. The Anaan arrived safely in Corfu, and Ezio promptly made arrangements to sail to Athens, and from there to Crete, and then Cyprus. Not long after departing from Crete, Ezio's ship ran into a storm, and was forced to dock at Chios for minor repairs.
Finally, Ezio arrived at Cyprus, where he spent some time exploring the island, including the Templar's archive. However, as he experienced more delays, it became apparent that the Venetian authorities stationed in Cyprus were intervening with his journey. Finally, Ezio took matters into his own hands and attempted to "acquire" a small ship of his own, so he could continue on to Masyaf.
No sooner had he found a seaworthy vessel was he attacked by a mysterious man, whom Ezio thought he recognized. The commotion caused by their fighting attracted several members of the island's Night Watchmen, and Ezio, along with his mysterious assailant-turned-ally, fought off the guards. As the last man fell, Ezio was stabbed in the side and fell unconscious. When he awoke, Ezio found himself on a ship headed for Acre, manned by none other than the pirate captain he had defeated some months earlier.
Ezio arrived in the city of Acre ten months after leaving Rome. After spending a week there, Ezio was informed that the road to Masyaf was filled with foreign bandits and mercenaries. He also wrote a letter to Claudia, informing her of his journey so far and that, should he not survive, she should not seek vengeance. Shortly thereafter, he continued his journey to Masyaf.

Templars leading Ezio to a plank

Ezio arrived at Masyaf in March 1511, and found the town to be crumbled and largely abandoned. Upon making his way to the fortress, Ezio was ambushed by the town's Byzantine Templar garrison, under the command of their captain, Leandros. Overrun and outnumbered, Ezio was captured by the Templars and lead onto a plank to be hung from the fortress' watchtower. However, as Leandros put the noose around Ezio's neck, Ezio attacked Leandros, threw the noose about Leandros' neck, and eventually escaped along the outside of the tower.
Ezio quickly made his way back to the battlements, where he retrieved his weapons. He then made his way beneath the castle, to the doors of Altaïr's library, where he learned from a worker that Leandros had the journal of Niccolò Polo in his possession, which supposedly led to the keys needed to open the library's door. Ezio left the fortress, and pursued Templar Captain, who had escaped by carriage.^[

Ezio assassinating Leandros

Ezio managed to hold onto a rope trailing from the carriage, and dragged himself up to the carriage itself. Leandros escaped onto the carriage of one of his men, and the chase continued, with each carriage jostling for space on a narrow cliff path.
Eventually, a well-placed bomb sent Ezio's carriage over the edge, severely injuring him, though he persistently continued to follow Leandros. Fighting his way through a nearby village, Ezio confronted and assassinated Leandros, claiming the journal for himself.

Settling into Constantinople

"Welcome to Galata district. For centuries it has been a home to orphans from Europa and Asia alike. You won't find more diversity anywhere else in the city. And for that reason, Assassins make it their home."

―Yusuf welcoming Ezio.

Having obtained the journal, Ezio made his way to Constantinople by ship, where he hoped to find those Masyaf Keys the Templars had not already obtained. As they neared the port, Ezio briefly spoke with a fellow passenger, a young man who claimed to be a student. Ezio spoke to him of how he spent his own youth, until a woman on the ship caught his attention. Disembarking the ship, Ezio was greeted by the leader of the local Assassin guild, Yusuf Tazim.

Yusuf welcoming Ezio

Yusuf informed Ezio of the state of affairs in the city and of how the Byzantine remnants fought with the Ottomans for control of the city. Later, Ezio was introduced to some of Yusuf's men, and was advised to get new equipment.
When the two met again, Ezio was provided with an Ottoman hookblade and was taught on its use by Yusuf. The two then aided in the defense and reclamation of two of the Assassin dens in the city. Ezio additionally met with Piri Reis, another Master Assassin in the city. Together with Piri, Ezio found Niccolò Polo's old trading post, which was inhabited by the Venetian bookseller Sofia Sartor; the woman who had caught Ezio's eye on the ship into the city.
Locating a secret passageway beneath the trading post, Ezio flirtingly suggested they both investigate, but was politely rebuked. He then entered the underground cavern, successfully obtaining his first Masyaf Key, as well as an encrypted map, which he eventually managed to decode with Sofia's help. Over time, Ezio started to develop feelings for Sofia, but could not bear to tell her about his Assassin affiliations.

Working with Prince Suleiman

"For now, keep an eye on Tarik and his Janissaries. They spend much of their free time in and around the Bazaar."

―Suleiman instructing Ezio.

Ezio continued to aid the Assassins in the city while Sofia worked to uncover the location of the remaining Keys. At one point, Ezio disguised himself as a minstrel, and prevented an attack on the young Prince Suleiman at Topkapı Palace; whom he recognized as the "student" from the ship he had entered the city on. After becoming acquainted with Suleiman, Ezio helped to uncover those behind the attempted assassination.

Suleiman conversing with Ezio

Their investigations led them to Tarik Barleti, Captain of the Janissaries responsible for Suleiman's protection, and supporter of his father, Selim I. After observing an exchange of weapons between Tarik and Manuel Palaiologos, heir apparent of the now-defunct Byzantine throne and member of the Templar Order, Ezio was tasked to kill Tarik by Suleiman.
Ezio carried out the assassination, only to discover Tarik had been working to apprehend Manuel and his associate - Shahkulu - "where they felt safest". Remorsefully, Ezio asked for Tarik's forgiveness, before delivering the news to Suleiman.

Journey to Cappadocia

"There he is. The monster I came to kill."

―Ezio when confronting Manuel.

Ezio leaving Constantinople with Piri Reis

After obtaining the four Keys still within Constantinople, Ezio traveled to Cappadocia, the location given to him by Tarik, to confront Manuel Palaiologos. Before he could depart however, he was intercepted by Yusuf, who informed him that the Janissaries had raised the Great Chain across the mouth of the Golden Horn to prevent him from leaving the city. Yusuf provided Ezio with a sizable bomb, claiming that it was significantly more dangerous than their usual explosives.
Ezio proceeded to the port, where he destroyed the Great Chain with Yusuf's special bomb, and burned the numerous Templar ships that guarded the harbor using Greek Fire.
Arriving in Cappadocia aboard Piri Reis' ship, Ezio sought to make contact with Tarik's spies, who were already in the city. However, he soon learned that many of Tarik's men had already been discovered, apprehended, and executed by the Byzantines. He arrived just in time to prevent the execution of the remaining spies, engaging and eliminating Shahkulu in open combat.

Ezio facing Manuel Palaiologos

With the spies safe, Ezio proceeded to detonate the city's ordinance supply and, in the ensuing panic, gave chase to Palaiologos. Confronting him at one of the city's docks, Ezio killed him and claimed the fifth and final Key. Before he could leave however, he found himself confronted by Suleiman's uncle and heir-apparent to the Ottoman throne, Ahmet.
Revealing his own Templar allegiance, Ahmet demanded Ezio to hand over the Key, lest harm fall upon Sofia Sartor. Angrily, Ezio pledged vengeance should any harm come to her, then made his way back through the now smoke-filled city to his ship, and to Constantinople.

Fight with Prince Ahmet

"Now should be a time for remembrance and mourning, I know... but our enemies do not permit us that luxury."

―Ezio before confronting Ahmet.

Ezio rallying the Assassins against Ahmet

After arriving in Constantinople, Ezio hurriedly made his way to Sofia's bookshop. He found that the place had been ransacked and Yusuf, whom Ezio had asked to look after Sofia during his time in Cappadocia, had been killed. Upon discovering Yusuf's dead body, Ezio gave him a final blessing before shutting his eyes. Declaring a renewed vengeance against all those who dared to cross the Assassins, Ezio collected the remaining Keys and prepared to ambush Ahmet during the exchange.
However, Ahmet held Sofia hostage atop Galata Tower, and Ezio was forced to give him the Keys in order to rescue her. The hostage turned out to be Azize, one of Ezio's fellow Assassins, and Ezio saw Sofia was being hung in a courtyard.
After parachuting down towards her, and after ensuring that she was fine, Ezio boarded a carriage with to pursue Ahmet, who had already hurried off towards Syria to find the library and unlock its contents.
After a lengthy ride through the country, which left Ezio essentially parasailing to hang onto their carriage, he managed to grab Ahmet and the two struggled as they both went flying off a cliff. Ezio subdued the prince and opened a parachute to save them both.
As they both recovered from their rough landing, Ezio and Ahmet saw an army arrive with Selim at its head. Selim explained that the Sultan had chosen him over Ahmet, and proceeded to strangle his brother and throw him off a cliff. Selim spared Ezio, having heard good things about him from his son Suleiman, but ordered him to stay out of Constantinople.

Ezio speaking to Desmond

After traveling to Masyaf with Sofia, Ezio used the five Keys to open the door to Altaïr's library. Ezio discovered there were no books, only the body of the former Mentor, with a memory seal in his hand. The seal revealed Altaïr's final moments, and the location of his Apple at the back of the library.^[14]
Ezio moved towards the Apple, but refused to take it, believing he had seen enough for one life. The Apple emanated a wave of light, and Ezio began speaking to Desmond. Acknowledging he was a conduit for a message, Ezio removed his bracers and sword to declare the end of his life as an Assassin. He then encouraged Desmond to make his life's sufferings worth it, and told him to listen.

Return to Constantinople

"Prince Suleiman knows of your return and has provided you with a safe-conduct. But his father is adamant that you should not remain long."

―Azize to Ezio.

After their visit to Masyaf, Ezio and Sofia returned to Constantinople to set their affairs in the city to rest. Despite Selim ordering Ezio never to return, Suleiman managed to secure Ezio a brief visit, as long as he behaved himself.
Ezio made sure that Dogan, the new leader of the Turkish Assassins, was able to competently command the Assassins' Guild there. Ezio also oversaw the selling of Sofia's bookshop to Azize, the Assassin who had been kidnapped by Ahmet and held at the top of Galata Tower as a decoy for Sofia. The bookshop was used as an outpost for the Assassins, and Ezio stored the Masyaf Keys in the chamber where he had found the first key, underneath the bookshop.

Later life

Settling down

"I knew I would not have enough time to do everything. Now I worry I do not have enough time to do anything."

―Ezio Auditore during his later years.^[src]

Ezio tending to his vineyard

Ezio and Sofia married in Venice. They had a daughter, Flavia, in May 1513, and a son, Marcello, in October 1514. By 1524, a retired Ezio lived with his family in a villa in the Tuscan countryside. There, he tended to a vineyard, and often spent time in his study, writing his memoirs.

Final visits to Leonardo

"I’ll tell you a secret. All my life—while I thought I was learning to live, I have simply been learning how to die."

―Leonardo's words on dying.

By 1519, Ezio had suffered a chest infection, and as a result developed a serious cough. This is likely hypersensitivity pneumonitis, also known as wine-grower's lung, due to his time in the vineyard.
A visit from Machiavelli revealed that their mutual friend Leonardo was dying. The pair traveled to Amboise in France to the manor Clos Luce, where Leonardo was staying.
Ezio learned that his friend wished to travel outside of the manor to places like England or even back to Venice where he hoped to sell his submarine idea, seeing as he was disappointed with his patron's last creation, a giant mechanical lion.
The pair stayed in France for another week, and visited Leonardo often. Upon their departure, rumors began to spread that King Francis was with Leonardo until he died, and had cradled his head. Ezio was disgusted by this rumor and believed that anyone, even a king, would do anything for publicity.

Teaching Shao Jun

"So I spent many years teaching men and women to think and act for themselves. First in Rome, then among our Brotherhood in Constantinople."

―Ezio expaining his deeds to Shao Jun.

One day in 1524, Sofia left with Marcello to visit Claudia, leaving Ezio to watch over Flavia. As Ezio started harvesting the crops, he called for Flavia to stay where he could see her. However, as he worked, he saw a mysterious cloaked figure approach Flavia. Panicking, he sprinted over to them, seizing the stranger by the collar, but pausing as he noticed the Assassin insignia on the necklace she wore.
Afterwards, the Assassin introduced herself as Shao Jun, a Chinese Assassin, who had traveled to Italy with her Mentor to learn of methods to unite the Assassins of her homeland. However, Ezio refused to be involved, though he allowed her to stay in the villa for the night on Sofia's insistence.

Ezio and Jun in Florence

The following day, Ezio found Jun sitting in his private study, reading a letter he had been writing. Infuriated, he ordered her out of the room, and insisted that she leave the villa.
However, Jun thoughtfully recited to him the words that he had written, wishing to understand their meaning. Ezio finally consented and invited her to accompany him into Florence while he ran errands. On the journey there and back, he finally spoke to her of the importance of love in the Assassin Order, saying that if she could support that which inspired hope in her people, she would succeed.
However, the two of them were ambushed by a Chinese Imperial soldier in Florence. Jun explained that she was a concubine who had escaped by joining the Assassin Order, and the soldier who attacked the two worked for the Chinese Emperor. Correctly expecting another attack at the villa, Ezio had his family evacuate to Niccolò Machiavelli's home, while he and Jun stayed behind.
Ezio and Jun were able to defend against the attack later that night, and in the morning, Ezio gave Jun a small chest before her departure, telling her only to open it if she lost her way. He had known from the start that the chest – which happened to be of Precursor origin – was always empty, to teach Jun to accept the responsibility that only she could decide which path to follow, the same path of blood that Ezio had taken. Although he had seen the rage and anger behind her eyes and tears, he could not encourage Jun to seek revenge, for it was her that would fulfill her own destiny.

Death

"I am home."

―Ezio to Sofia in Florence.

Ezio passing away on the bench

In his final hours, Ezio chose to go to Florence with Sofia and Flavia while they went shopping. Ezio sat down on a bench, feeling ill, and shrugging off Sofia's concerns that he should have stayed home, stating "I am home."
While Sofia and Flavia went to buy groceries, a young man approached Ezio, thoughtfully berating the women of Florence. Ezio wearily responded by implying the man was the problem, not the city. Immediately afterward, Ezio began panting and holding his chest in pain.
The young man quickly grabbed Ezio's hand and told Ezio to have courage. He told Ezio to "get some rest", and then left. Ezio looked back at him angrily, but calmed down just as quickly. Breathing heavily, Ezio looked over at Sofia and Flavia, smiling, before resting his head against the back of the bench, and passing away peacefully.