Joseph, one of the founders of the twelve tribes of Israel, possessed the Shroud of Eden. Moses led the Hebrew slaves out of Egypt and back to Israel with a Staff of Eden. David, the second King of Israel, possessed the Shroud of Eden. David's son Solomon built a temple to house the Ark of the Covenant, which contained an Apple of Eden.
During the Roman Empire's occupation in the 1st century CE, David's descendant Jesus possessed the Shroud, which the Templars crucified him to gain possession of. However, his disciples recovered it and tried to resurrect him with it. Jesus' cousin John possessed a Staff, which presumably passed to his disciple Peter and his successors to the Papacy.
During the Middle Ages, the Crusader and Saracen occupiers waged wars to control Jerusalem. The Templars became a public Order of Knights after finding the Apple in Solomon's Temple. Despite Jerusalem falling under Saracen control during the Third Crusade, the Knights Templar still had a presence there, guarding the prize that made their fortune and power. Altaïr Ibn-La'Ahad, Malik Al-Sayf and his brother Kadar were sent to steal the Apple: despite Altaïr's arrogance bungling the operation, causing Kadar's death, Malik managed to recover the Apple.
To redeem himself, Altaïr was sent to assassinate the nine leaders of the Templar Order: he hunted for Talal and Majd Addin in Jerusalem, and Garnier de Naplouse, William of Montferrat and Sibrand in the Crusader-held city of Acre. Finally, he was sent to kill Robert de Sable in Jerusalem, but the Templars were prepared for him and used Maria Thorpe as a decoy. Altaïr rode to Arsuf, where de Sable was attending a battle with Richard I of England, and defeated him in combat.
In 1511, Jerusalem was controlled by the Mamluks, who arrested the Assassin leader Mujir. He was rescued by Ottoman Assassins sent by Ezio Auditore da Firenze, who continued to expand the Order's presence in Jerusalem. Ezio and Sofia Sartor also stayed in Acre during their quest to open Altaïr's library beneath Masyaf.