Previous entries here, here, and here.
Now we'll conclude our look at the Spanish imperial Deep State with a survey of the initial rise, the stagnation / decline, and the collapse of its power over purely political affairs.
At the outset, Iberia was not yet fully liberated from the Moorish conquerors, as the Emirate of Granada remained in the deep south. So the main internal threats to the centralizing state, which was coalescing around the Catholic Monarchs, were the foreigners who had originally invaded, or who had come along with the invaders to help administer their empire. That was mainly the Muslims and Jews.
Under its first Grand Inquisitor, Torquemada, the Inquisition was instrumental in expelling the Jews in 1492. Muslims were treated less severely, since they were the still somewhat powerful invaders, whereas Jews were easier to drive out, as they were mere professionals and administrators of their Muslim rulers. At first Muslims were forced to convert to Christianity or leave Spain, during the early 1500s.
One century later, in 1609, even the converts (Moriscos) were ordered to leave as well. However, some of them returned, and in 1628 the local inquisitors in Seville were ordered not to hound them as before. This shows how the empire was nearing its peak / plateau stage in the middle of the 17th C., as it would have been inconceivable that Torquemada would have given them such a light touch over 100 years earlier.
Before getting to that stagnation phase, though, let's look at the power of the Inquisition in another way -- the period when the Grand Inquisitor was also the regent of the Castilian kingdom (i.e., the acting ruler). Cisneros was appointed to lead the Inquisition in 1507, and by 1516-'17 he was also the regent of the kingdom. This was not like when George H.W. Bush headed the CIA for a brief moment, and then became president over a decade later -- this was at the same time, and having headed the Deep State for nearly a decade.
And to drive home his role as the controller of internal enemies of the centralizing state, as regent he oversaw the conquest of Navarre by Castile. The Navarrese were not Jews or Muslims -- but they were weakly integrated into the state, belonging to the northeastern region formally controlled by the kingdom of Aragon. And they were still occasionally rebelling against Castilian dominance, so Castile subdued them by force, overseen by not only the political leader but the leader of the religiously based Deep State. If they belong to the same religion as the central state, then just slander them as not-good-enough members of the religion, as heretics, as blasphemers, as apostates, and so on and so forth.
After Cisneros died, Adrian of Utrecht -- a Dutchman -- took his place as Grand Inquisitor in 1518. Soon after, from 1520-'22, Adrian was also the regent of the empire, during which time he oversaw the continuation of the conquest of Navarre.
Even closer to home in Castile, he oversaw the suppression of the Revolt of the Comuneros, which did not involve Jews or Muslims, nor even the weakly integrated northeasterners. It was a local revolt against foreign rule: the new King was also a Dutchman and the Holy Roman Emperor (soon-to-be Charles I of Spain). On top of that, it was a succession crisis, as the rebels wanted Charles' mother, Queen Joanna, to rule on her own (she had been confined for madness, and de facto did not rule). Joanna had a much more direct and local bloodline to the founding of the empire, as she was the daughter of Isabella I.
But as empires expand and begin to administer international polities, they often absorb the elites of other realms, including at this point when the non-Iberian House of Habsburg was about to control the Spanish Empire during its Golden Age. Already a Dutchman was regent, as well as the Grand Inquisitor -- why not also let a Dutchman be their king?
In the Comunero Revolt, the enemies of the centralizing state were nationalists or nativists, who were against the increasingly international character of their growing empire. There are all sorts of enemies to the centralizing state of a growing empire -- literal foreign invaders, domestic separatists, nativists -- it gives the security apparatus plenty of work to do, and it means they have to rationalize their mission in increasingly twisted ways. It's no longer as simple as, "Christians safe, Muslims and Jews threatening". Whoever poses a risk to the central authority of the Catholic imperial leadership, is a heretic.
After leaving Spain, Adrian became Pope in 1522, the only Dutchman to fill that office. Regent of the preeminent empire in Europe, head honcho of its Deep State, and then leader of the Catholic Church, as well as the political leader of the Papal States in Italy -- all within a few years. This is what central legitimacy and authority looks like.
One of the last displays of the growing power of the Inquisition was in the 1560s and '70s, when the Grand Inquisitor, Valdes, launched a heresy trial against the sitting Archbishop of Toledo -- the #1 ranking leader of the Catholic Church in Spain -- Carranza. Surprise, surprise -- Carranza was from a noble Navarrese family, who grew up during the Spanish conquest of his land. Maybe the Grand Inquisitor thought that made him still a threat, if he were nursing a grudge. At the least, he was more sympathetic to foreign thinkers like Erasmus, which brought charges of supporting Lutheranism. Remember: ideas don't matter, they were afraid that he would allow in unwanted foreign political influence, not airy-fairy crap about the nature of Christian worship or whatever.
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The Deep State of any empire is not an all-powerful entity, and its leaders are political appointees. It's not uncommon for the leadership of the Deep State to change when the political leadership changes. This was no less true for the Spanish Empire.
It's hard to imagine Torquemada or J. Edgar Hoover getting kicked to the curb by the political leaders, but they were heads of the Deep State at the powerful outset. FBI Director Comey was unceremoniously fired by Trump, and beginning in the early 1600s several Grand Inquisitors were forced out of the office when political leadership turned over or they lost favor (Niño de Guevara, Aliaga, and Sotomayor).
The first sign of the Inquisition's stagnating political power came in the 1660s, when Nithard was the Grand Inquisitor, as well as the de facto prime minister (the royal favorite of the Queen and Regent). His reign came just after Portugal won its independence from Spain in 1640, after having been conquered in 1580. That is a strong signal that the Spanish Empire is past its glory days. But then Nithard signed the Treaty of Lisbon (1668), whereby Spain got basically nothing from Portugal, in return for Spain giving up a major Iberian possession and officially recognizing the new Portuguese royal house. For such weak foreign policy, Nithard was kicked out in a bloodless military palace-coup.
The next inflection point in the decline of the empire was the War of Spanish Succession in the early 1700s. The last Habsburg monarch named his French Bourbon son as his successor, but an Austrian faction wanted Habsburg rule to continue in Spain. This war ultimately brought about the end of the Habsburg era, and the start of the Bourbon era. During the war, the Austrian faction was most popular in the weakly integrated northeast of Spain.
Even the Grand Inquisitor himself, Mendoza, favored the Austrian side -- however, he was accused of treason for that, fled to exile for 7 years, and was only allowed to serve as a bishop on his return. Not even an archbishop, let alone head of the Inquisition. But that's what the Deep State gets when it tries to interfere in a political succession crisis, on the illegitimate side at that, and well past the peak of imperial power. This marks an irrevocable loss of the legitimacy and authority of the Inquisition.
As a wonderful natural experiment, the regency board during the early stages of the war included both the G.I. Mendoza and the Archbishop of Toledo, Portocarrero. Both big religious figures, the former who sided with the Austrian faction, and the latter who not only supported the Bourbons but was instrumental in persuading the last Habsburg to name his Bourbon son as successor. Mendoza was only on the board for a few months, while Portocarrero was regent for several years until the Bourbon successor arrived in Spain. So while the Catholic Church may have maintained some degree of power over political affairs, the Deep State was losing it.
By the late 1700s, the Grand Inquisitor was reduced to adding Enlightenment thinkers onto its list of prohibited books, which was not successful anyway. That included G.I. Beltran's 1775 heresy trial against Olavide, an Enlightenment reformer (of Basque ancestry).
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All empires collapse, and so do their Deep States along with them. Ours will be no different.
The Spanish Empire collapsed during the early 1800s, as Spain itself was occupied by Napoleonic France, all of its New World colonies fought and won wars of independence, and it ceded further New World territory to the American Empire (Florida). America picked up the leftovers later in the century (Spanish-American War, getting the Philippines, Cuba, and Puerto Rico).
The Inquisition was first abolished during France's occupation of the peninsula (1808 - 1814), and far from bouncing back strongly with the expulsion of the French and Napoleon's downfall, it oscillated between bouts of abolition and tepid re-establishment, being abolished for good in 1834.
The Grand Inquisitor when Napoleon invaded, Arce, gave pro-French sermons while his country was under foreign occupation. Not only did he not resume leadership of the Inquisition, which was more or less defunct anyway, he had to resign his offices within the Catholic Church as well (Archbishop of Zaragoza, and Patriarch of the West Indies). He was forced into exile for the rest of his life. So much for the all-powerful nature of the Deep State.
Wikipedia says the Inquisition condemned the guerrilla warfare by civilian Spaniards against the invading French army, which was the only reliable defense that Spain had against France, who easily defeated them in conventional battlefield warfare. There's no citation, and the Inquisition was formerly abolished at the time, so maybe this means the former leaders of the Inquisition (like Arce) still met and issued opinions to the public, including this one. If that's true, the reason is easy to surmise: guerrilla leaders were acting outside of the central state, and were therefore a threat to its authority and legitimacy, especially since they were so successful, while the central regular military was failing.
Getting on the wrong side of a war of national liberation in your own territory, just because the winners are not part of the central state? That's an easy way to shred what little remains of your credibility, legitimacy, and authority. It's not really treason, since the Inquisition did not side with France over Spain, they were opposed to those outside the central state playing the main role in defending the integrity of the state's territory. Nevertheless, it shows how useless the Deep State had become by that point, so there was no hope of its preservation as the empire only continued to disintegrate.
As during the War of Spanish Succession, there were several influential figures of the Catholic Church who were regents during the French invasion, but they were not also on the Inquisition. This included a lowly bishop Quevedo in 1810, and the Archbishop of Toledo, Luis Maria de Borbon, from 1813-'14. The latter went on to abolish the Inquisition in 1820.
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Without going too much into the history of the lesser arm of the Spanish imperial Deep State -- the Santa Hermandad -- I'll simply note that it parallels that of the Inquisition. It was formed in 1476, as a result of the Civil Wars of the Reconquista (1350 - 1479), when the new leaders of the increasingly central state wanted a national police force that was under their control alone, not regional police forces that could be controlled by lesser royalty or regional nobles. It was used to harass political rivals, shake down wealthy people, and build their own power base.
It waned in power by the early 19th C., and crucially played no role in the liberation of Iberia from the Napoleonic invasion. As with the impotence of the Inquisition during this crisis, the absence of the Santa Hermandad shredded what was left of its credibility and authority. Technically, its purpose was internal policing, but when Napoleon occupies your country, you should re-focus your efforts to drive out the invaders.
Worse still, the forces that did drive out the French were guerrillas -- the very type of unit that a strong national police force would have persecuted and locked up, for practicing vigilantism. That is, for horning in on the business of the Hermandad. By 1844, they were replaced by the Guardia Civil -- a national gendarmerie, without the holy rationalization of the earlier imperial Deep State.
No more empire, no more obsession with controlling internal enemies of the central state, which only gets less and less centralized during imperial collapse.
Importantly, neither the Santa Hermandad nor the Inquisition was re-established during the Franco era in the 20th C. Although Franco had the support of the military, was a law-and-order leader, and was still based in Castile and facing rebels from the historically weakly integrated northeast, he was still ruling a full century after the collapse of the Spanish Empire. And so, none of its organs stood any chance at being reincarnated, as though being a right-wing leader gave someone magical powers.