The Tribunal of the Holy Office of the Inquisition, commonly known as the Spanish Inquisition, was a tribunal established in 1478 by Ferdinand II of Aragon and Isabella I of Castile, the King and Queen of Spain. It was intended to maintain Catholic orthodoxy in their kingdom, and to replace the medieval inquisition which was under Papal control. The Inquisitors were known for their unnecessary amount of violence towards non-Catholics.
The first Inquisitor General was Tomás de Torquemada, who in 1491 was persuaded by Rodrigo Borgia to arrest a number of Spanish Assassins after giving him a list of supposed heretics. After Luis de Santángel requested his aid, the Italian Assassin Ezio Auditore da Firenze traveled to Spain to free his brothers and killed several Inquisitors, namely Gaspar Martínez, Pedro Llorente and Juan de Marillo. However, Ezio spared Torquemada when he learned he was not a Templar, and had been manipulated by Rodrigo into arresting the Assassins.
The Assassins eventually killed Torquemada in 1498, while Luis began poisoning Queen Isabella in an attempt to end the Inquisition, having learned that Cesare Borgia, with the Church's backing, had been threatening her to facilitate the Inquisition's spread into Portugal. The Italian Assassins sent by Ezio continued Luis' work following his death. Regardless, Manuel I of Portugal chose to allow the Inquisition into his country, and opted to banish the Jewish population. The Assassins helped many flee to Constantinople, and assisted those who could not to fight for themselves.
The ruler of the Ottoman Empire, Bayezid II, accepted the influx of refugees, knowing that the intellectuals among them would ultimately benefit his empire. Hoping to spread their influence and weaken the Ottoman Empire, the Templars hid saboteurs and dissidents in the crowds; however, this plan was thwarted by the Italian Assassins, who eliminated the Templar agents and ensured the refugees were welcomed.