It is difficult for us to understand the Spanish Inquisition because we are so used to the separation of church and state in modern times. During the time in which the Inquisition in Spain was most active (1480-1600s), however, heresy was considered a crime similar to political treason because the monarchies of Europe and the Catholic Church were so closely linked, and according to Roman Law torture could be used to extract confessions of guilt in cases of capital crimes. While forced conversions, torture, and the executions that took place during the Spanish Inquisition can never be excused, it is necessary to understand what was going on in Spain and in the Mediterranean at this time in history to see it in context and to distinguish the truth from the lies that have been told for 500 hundred years about this period of Spain’s history.

Contrary to what many believe, the Spanish Inquisition did not target Protestants or people who had been Jєωιѕн or Muslim from birth. Rather, it was concerned with the issue of heresy and apostasy in Spain. According to the Catechism, “Heresy is the obstinate post-baptismal denial of some truth which must be believed with divine and catholic faith, or it is likewise an obstinate doubt concerning the same; apostasy is the total repudiation of the Christian faith.” (CCC 2089) In the 1300s there were many Jєωs in Spain who had converted to Catholicism, called “conversos,” who were believed to have committed apostasy by returning to the practice of Judaism. James Michener points this out in his book Iberia:
“So far as I was able to ascertain, no Jєω was ever executed by the Inquisition. If a man under investigation could say simply, ‘Yes, I’m a Jєω and have never been otherwise,’ his gold and silver were confiscated and he was banished from Spain, but he was in no way subject to the Inquisition and certainly he was never burned. The Jєωs who did suffer, and in the thousands, were those who had at one time been baptized as Catholics, had been legal Catholics and had committed apostasy by reverting to Jєωιѕн practices. These were rooted out with great severity, but when they were burned, it was as Catholics, not as Jєωs.”(1)  

By the 1400s the conversos had gained a lot of power in Spain – in business, property, and government. Queen Isabel I of Castilla (1451-1504) was informed that many of the conversos were not sincere Christians, that they had converted only for the advantage it would give them in society, and that they could not be trusted in a time of war.(2)  During this time tensions were mounting all over Spain between Catholics and Jєωs, and violence and riots were becoming commonplace. In the year 1478 Isabel and King Fernando II of Aragon asked Pope Sixtus IV for the authority to begin an Inquisition in Spain (there was already an Inquisition governed by the Pope to defend the Church against heresies in other parts of Europe). Pope Sixtus IV granted them permission in 1478, but Isabel and Fernando decided to put off beginning an Inquisition in Spain. For the next two years they tried to improve catechesis among the conversos, hoping that this would bring them to accept the fullness of the faith they had been baptized in. Meanwhile, Muslims still held Granada in the south of Spain, and could at any time invade the rest of the peninsula with reinforcements from Africa, as they had 700 years before. Moreover, there was a very real threat of Ottoman attack along the coastlines of Southern Europe, where Christians lived in fear of being killed or sold into slavery. In fact, in August of 1480 Ottoman forces attacked the city of Otranto, in Southern Italy (which was under the joint rule of Naples and Aragon), and killed thousands of its inhabitants. The Ottoman soldiers entered the Cathedral in Otranto and killed Archbishop Stefano Agricola and others inside, while Bishop Stephen Pendinelli and the garrison commander, Count Francesco Zurlo, were sawn in two alive. Then, on August 13th 800 citizens of Otranto were taken to the hill of Minerva and beheaded when they refused to convert to Islam. (The Martyrs of Otranto were canonized on May 12, 2013.)(3)  The next month, on September 26, shortly after the news of this massacre would have reached Spain, Isabel and Fernando instated the Inquisition in Spain, and appointed the members of its first Tribunal in Castilla: Cardinal Mendoza, Fray Tomas de Torquemada, and two other Dominicans, Fray Miguel Morillo and Fray Juan de San Martin.

Typically, when the Tribunal began in a city an “Edict of Grace” was announced. These gave people an opportunity to confess and be reconciled with the Church (sometimes this was done three times). In the course of the Tribunal’s proceedings two doctors examined each accused person to make sure they were of sound mind before they were questioned, and if the accused had been influenced  by a priest, teacher, or even parents, this was considered an extenuating circuмstance. The accused was allowed to make a list of all of his enemies in order to prevent false accusations, and mistreatment of the Jєωs and false accusations of conversos could be punishable by death. In 1482 Tomas de Torquemada was appointed Inquisitor General of Castilla and Leon. Contrary to what many historians have written about Torquemada, he did away with many of the abuses of his predecessors and he reformed both the judicial system and the prison conditions of the Inquisition. In fact, civil prisoners of his time would sometimes pretend to be heretics to have their cases transferred to the Inquisitorial courts.

The Black Legend is the reason many facts regarding the Spanish Inquisition have been grossly exaggerated for hundreds of years. It refers to an attempt by some Protestant scholars in the 1500s and 1600s to discredit Spain and Catholicism by spreading lies about Spain, the Spanish Inquisition, King Felipe II, and Catholicism. According to Edward Peters, there was a conspiracy to create a false image of Spain as a symbol of evil, brutality, political and religious intolerance, and artistic repression, which lasted for hundreds of years.(4)

http://www.catholicnewsagency.com/cw/post.php?id=719

I posted this so you could get a better idea of what theInquisition was all about.