Its more than just crusades. By the late Middle Ages, the Church was a very corrupt institution - half the Popes were either murdering their opposition (Borgias, anyone), or having children out of wedlock, or engaging in intense bribery -- (indulgences, anyone), that when there was push-back in the form of Martin Luther, there was equal and violent push back by the Church in the form of the Inquisition. It took hundreds of years for that to settle out, and it has settled out. The Pope we have today is such a holy man and would have been totally out of place in the Middle Ages.
Mohammed and Charlemagne Revisited:
The History of a Controversy
by Emmet Scott
New English Review Press · 2012 · 270 pages
$19.95 · Kindle version $9.95
Mohammed & Charlemagne Revisited by Emmet Scott
Throughout the coastal areas surrounding the Mediterranean Sea, archaeologists have uncovered a layer of subsoil that was deposited over a period of three hundred years beginning in the middle of the seventh century AD.
This stratum, named the “Younger Fill” by the geologist Claudio Vita-Finzi, covers the ruins of all the major cities and settlements that were established along the Mediterranean littoral during classical antiquity. It stands as a coda to Graeco-Roman civilization. For three centuries after the year 650 the archaeology of the region is all but barren. Wastelands or severely diminished primitive settlements have replaced the formerly great cities of the Roman Empire and the Near East.
One might surmise that the Younger Fill is the result of some yet unidentified climatic trauma that afflicted the entire Mediterranean basin. However, the same phenomenon has been observed in an entirely different watershed: Mesopotamia, the land drained by the Tigris and Euphrates in what is now Iraq, and also including the coastal regions adjoining the Persian Gulf.
During the same period — from the middle of the seventh century until the middle of the tenth — archaeology in the entirety of Europe and the Middle East virtually disappears. This civilizational interruption might be thought a result of the Dark Ages in Europe, except for the fact that it includes areas of the Middle East which were never part of the Roman Empire, and where advanced cultures independent of Rome and Greece had flourished.
What all these areas have in common, of course, is that they were conquered by the Arabs during the initial period of Islamic expansion, when the Near East, North Africa, and Iberia were subjugated within the space of less than a century.
Islam came to the Mediterranean and left as its principal legacy the Younger Fill.
http://gatesofvienna.net/2012/08/who-really-killed-the-pax-romana/
Are you referring to the Spanish Inquisition?
Recent scholarship debunks much of "The Black Legend."