The Truth about the Inquisition requires extensive research on reliable sources

Protestants attacking the Catholic Church often use the Holy Inquisition. This allegedly proves the Catholic Church does not belong to God but to the devil since the church killed many people through the Inquisition. 

According to an expert, Professor Diane Moczar in her book, Seven Lies About Catholic History: Infamous Myths about the Church’s Past and How to Answer Them on page 96:

“By the thirteenth century, the task of confronting heresy had devolved upon the new mendicant religious orders founded by St. Dominic and St. Francis, which were mainly dedicated to preaching the Faith. The aim of these Dominican and Franciscan inquisitors was the conversion of the heretic, not his extermination (in either of its meanings).” 

It is clear that the Inquisition has a different purpose. It was not made to kill people. 

Professor Moczar also clarified the Church does not kill. 

"One of the most famous inquisitor, Jacques Fournier (the future Pope Benedict XII), who interviewed some 930 suspected heretics during his career, never used torture; he got all the information he needed through skills andnot force. He assigned various penalties to those judged guilty, ranging from making a pilgrimage or wearing a cross to exile or imprisonment. Forty-two heretics he turned over to the secular authority for execution. (The Church itself did not execute; when a crime was judged worthy of death, the criminal was turned over to the state with a request for mercy. Since the crime in most such cases challenged secular authority in some way or was even considered high treason, the request for mercy was usually ignored.) (Seven Lies About Catholic History: Infamous Myths about the Church’s Past and How to Answer Them, Diane Moczar, Tan Books (September 1, 2010),  pp.88-89)

Thus, our Protestant friends must become honest just like the Protestant Professor Rodney Stark. In his book, Bearing False Witness: Debunking Centuries of Anti-Catholic History, we will learn that what others say about the Inquisition is not true.

In popular culture, the term “Inquisition” is nearly a synonym for torture. As John Dowling (1808–78) explained, “Of all the inventions of popish cruelty the Holy Inquisition is the masterpiece…. It was impossible for even Satan himself to conceive a more horrible contrivance of torture and blood.” Thus, as noted above, it has been taken for granted that many more poor souls died in the Inquisition’s prisons and torture chambers than survived long enough to go to the stake.

This may be the biggest lie of all!

All the courts of Europe used torture, but the Inquisition did so far less than other courts. For one thing, Church law limited torture to one session lasting no more than fifteen minutes, and there could be no danger to life or limb. Nor could blood be shed! There are, of course, very painful techniques that can be applied within these rules. But even so, torture was rarely used, perhaps because the “[i]nquisitors themselves were sceptical of the efficacy and validity of torture as a method of conviction.” (Bearing False Witness: Debunking Centuries of Anti-Catholic History by Rodney Stark)

The Holy See set up an office at the time of the Reformation, to review and pass judgment on the orthodoxy of religious statements and practices throughout the Church - the distant ancestor of our Congregation for the Doctrine of the Faith.  This did not have a lot of political or police power to enforce judgments.  Then, in the early 16th century, one of the kings of Spain (Ferdinand?  Philip II?)  set up an independent Spanish version, operated by the royal government.  There, in the wake of the new unification of Spain as a "Christian kingdom," with the attempt to expel Jews and Muslims from the peninsula going on, some officials were concerned that some people were claiming to be Christians or converts, who were really not genuine.  So the government decided it needed its own, tougher version of the Inquisition, to ensure religious unity for political purposes.  Most of the violence of the Inquisition is attributed to them.  (Our Jesuit founder, St. Ignatius of Loyola, and St. John of the Cross, among others, were both imprisoned several times by the Spanish Inquisition.)

St. Ignatius tells in his Autobiography about his own experience after his conversion, being harassed by the  inquisitors and imprisoned by them, in Alcala and Salamanca, because he was preaching and giving people catechetical instruction, without yet having a degree in theology and while still a layman.  You can find the Autobiography in any collection of St. Ignatius's works.  For St. John of the Cross, this would be in any biography of him; there is a new book by Fr. Thomas Dubay on Teresa and John of the Cross called Fire Within, which should tell you something about this experience.