During the early 16th century, after the Templars were driven from Italy by the Assassins, the members of the Templar Order were able to seize control of the remnants of the Byzantine Empire. Now in command, the Templars set up their primary headquarters at the underground city of Derinkuyu in Cappadocia, where the Byzantines' ultimate aim was to uproot the Ottoman Empire and retake control of Constantinople. For a time, however, they remained relatively quiet.
Search for the Masyaf Keys
Following the earthquake in Constantinople in 1509, Templars reappeared in the city under the Byzantine banner. Due to Sultan Bayezid II's disappearance from the city following the earthquake, the Byzantine Templars could easily integrate into the city and start their plans for taking over the Ottoman Empire, while operating from their headquarters in Derinkuyu. Initially led by Manuel Palaiologos, the Byzantine Templars quickly caught the eye of Prince Ahmet, Bayezid's son and supposed successor. Ahmet joined the Templar Order, and his youth and charisma allowed him to slip into the position of leader while Manuel was forced to become a second-in-command.
The Templars somehow recovered "The Secret Crusade", the journal of the Italian explorer and secret Assassin Niccolò Polo, from which they found out about the existence of the library of Altaïr Ibn-La'Ahad in Masyaf and the keys needed to open it. Ahmet placed Manuel Palaiologos in charge of the Masyaf expedition to find the Masyaf Keys throughout Constantinople, while Ahmet himself continued his plans to secure the Templars' power in the Empire.
By 1511, the Templars had managed to obtain one of the Masyaf Keys from underneath Topkapı Palace, and had taken full occupation of Masyaf. Without the other Keys in their possession, the Templars had resorted to digging their way into the library, with no success. In the winter of 1511, Ezio Auditore da Firenze arrived in Masyaf, also wanting to access the library. He was ambushed by Byzantine Templars led by Leandros, and was overpowered and captured. The Templars subsequently led him to Masyaf's watchtower, where he was to be hanged. At the very last moment, he fought back against Leandros, who was tying the noose around Ezio's neck. Ezio threw the noose around Leandros' neck instead, and Ezio jumped down to a scaffolding below. With no sign left of Ezio in the thick snowstorm that was brewing, Leandros instead decided to focus on other matters and was about to leave on a horse cart. Ezio gave chase, and jumped to a rope hanging on Leandros' cart, eventually procuring his own cart to keep up with his pursuit.
Leandros crashed Ezio's cart near Atlas Village in the mountains, and made his way into the village while sending the other Templars to deal with Ezio. However, the wounded Ezio made his way through the guards and into the village's center with some difficulty, coming to the area where Leandros had taken refuge. Leandros, sending more of his men at Ezio, was ultimately confronted and killed by Ezio on top of the village's watchtower, where Ezio took "The Secret Crusade" from him.
Struggle in Constantinople
In Constantinople, the Templars were still ever present, engaging in heavy combat with the Turkish Assassins, occupying numerous Assassin Dens throughout the city and searching for the secret locations in the city leading to the Masyaf Keys. The Templars discovered that two of the Masyaf Keys were located in the Yerebatan Cistern and the Forum of the Ox, but Ezio Auditore recovered the artifacts before the Templars could.
Ahmet personally devised a plan to have his nephew Prince Suleiman kidnapped at a feast in the Topkapı Palace, allowing Ahmet to "rescue" him and gain the Ottoman citizens' favor over his brother Selim for the Ottoman throne. However, Yusuf Tazim and the Turkish Assassins learned of the Templars' plan and plotted to stop their plan. With the help of Ezio Auditore, the Turkish Assassins—dressed as Italian minstrels—found and killed all of the Templars hidden amongst the party goers. Ahmet, whose Templar affiliation remained a secret, instead accused Tarik Barleti, the captain of the Janissaries, of being unable to stop the 'attack' of the Italian minstrels.
Some time later, Manuel journeyed to Constantinople to purchase guns from the Tarik and the Janissaries for his forces in Cappadocia. Accompanied by the Turkmen renegade and Templar Shahkulu, Manuel inspected the weapons in the city's arsenal and successfully closed the deal before returning to Cappadocia. Tarik was assassinated by Ezio Auditore some time later on Suleiman's orders, after the two came to the wrong conclusion that he was in league with the Templars when in reality, he had been spying on the Templars in Cappadocia in order to thwart them. His death was quickly believed to have been orchestrated by Ahmet, damaging his public image.
In 1511, the Assassins and Templars battled for control of Bursa. The Templars kidnapped Sultan Bayezid II's third son Korkuta, though he was saved by Assassins sent by Ezio Auditore da Firenze from Constantinople. Templars started to lose control of Bursa, and the Assassins moved in to take control.
Collapse of Cappadocia
In March 1512, Manuel and Shahkulu returned to Derinkuyu in Cappadocia, where they continued building up the Byzantine army's strength while capturing and executing numerous Ottomans.
Unbeknownst to the Manuel, Ezio Auditore had trailed him to there, and one of their captured Ottoman spies, a woman named Dilara, had managed to escape. Shahkulu, a sadist, was reveling in his public executions when Ezio air assassinated him from above, though much to the Assassin's surprise, Shahkulu's armor protected him from the strike. Ultimately, Ezio killed Shahkulu after a duel and simultaneously stopped the torture and execution of the Ottoman spies in the city.
The Templars panicked when Ezio Auditore blew up the ammunition and armaments hidden inside the city, and Manuel Palaiologos tried to calm the city's citizens. Upon spotting Ezio, Manuel fled and sent the Templars to kill Ezio. The Templar soldiers proved no match for Ezio, and the Assassin confronted Manuel after the latter ran to a dead end on a jetty. Manuel was easily slain and gave up his Masyaf Key to Ezio, cynical that he would survive long enough to enter the library. At that very moment, Ahmet arrived on the scene by boat, revealing his Templar allegiance and threatening to capture Ezio's love interest Sofia Sartor if Ezio did not surrender the Masyaf Keys.
Fall of the Byzantines
Ahmet returned to Constantinople not too long afterwards and sent a battalion of Templars to capture Sofia from her book shop. The book shop was guarded by Yusuf Tazim and other Assassins, though the Templars emerged victorious, killing Yusuf in the process. Upon discovering Yusuf's lifeless body, Ezio rallied the Assassins against Ahmet and the Templars, who had fortified themselves at the Harbor of Theodosius. When Ezio reached Ahmet, he furiously demanded for the whereabouts of Sofia, to which the latter reminded him that harming him would cost him the chance to save her. As Ezio let him go, Ahmet lectured that since they both dreamed of world peace, with only their methods differing, it was unreasonable for them to ever have been enemies in the first place. He then asserted his belief that even when people acquire the truth, they are reluctant to acknowledge it. This failed to sway Ezio from his convictions in liberty and diversity, and so without further ado, Ahmet moved on to his real point: an ultimatum demanding that Ezio bring the Masyaf keys to the Galata Tower, lest he have Sofia executed.
On the wall of the Galata Tower, Ahmet and a group of Templars waited for Ezio, who indeed arrived with the keys in exchange for Sofia. However, Ahmet instead had Azize dressed in Sofia's clothing with a bag hidden over her head held by the Byzantine soldier, while the real Sofia was being hanged on a nearby plaza. With this success, Ahmet made his leave out of the city with the Masyaf Keys, and started his journey to Masyaf to open the library.
Before he had even left the outskirts of Constantinople, Ahmet and his Templar entourage were tailed by Ezio and Sofia, the latter who had been rescued by Ezio, and a chase on horse carts ensued. The Assassin took out the other Templar horse carts, only to be knocked off his own carriage by Ahmet, but he managed to keep himself anchored to the cart with a rope. While Ahmet continued his way forward, with Sofia—now as the driver of Ezio's carriage—in rapid pursuit, Ezio deployed his parachute so as to safely tow behind his cart. After a long chase through the mountains, Ahmet obliterated Sofia's cart. Ezio landed on a nearby hill and from there jumped onto Ahmet's cart, causing the two to fall off a cliff side together.
The two continued to fight one another during their free fall, until at last when they neared too close to the ground, Ezio deployed another parachute to effect a safe landing, with Ahmet managing to hold on safely to him. They both landed safely, but showed signs of heavy fatigue. At that moment, Selim arrived with his army from battle with his father, and strolled up to Ahmet. At his brother's approach, Ahmet fearfully demanded for the presence of the Sultan, insisting that the Janissaries were to obey only his command, not Selim's. It was then that Selim, revealing that he in fact was now the Sultan, started choking Ahmet before throwing him off a precipice to ensure that there would be no conflicts for succession. With Ahmet's death, the Byzantine Templars were ultimately dissolved.