You want an explanation of the deepest, darkest issue of European history in 2,500 characters? Okay, short version! :)
The so-called Dark Ages were a time of poverty, plague, war, and death. Popes made efforts to reduce inter-Christian wars by calling Christians to war together on the same side against non-Christians in the crusades.
The Enlightenment brought new technologies that increased crop production and led to greater economic prosperity.
From a Jungian perspective, the dark fear of plague and death still haunted the collective unconscious of the European peoples.
From an economic perspective, until the 2nd industrial revolution (2nd half of the 1800s), a prosperous economy still required 90% of all people to work on farms or engage in labor so that a few could prosper. If Enlightenment ideals called for the education of all Europeans, then someone else would have to do the work (as serf or slave), and grabbing their wealth (through pillage or colonial exploitation) was the easiest way to gain enough wealth to lift up one's own people.
To justify this exploitation, it was necessary to pretend that people of other lands, other languages, other religions, or other colors were not human, or at least not fully human.
To not do this meant not to grow while one's deadly enemies were growing Europe was not unified. England and Spain and others were locked in a deadly competition, and focused their, and used unjust means to gain wealth to support their wars with one another in an awful drive for dominance.
How corrupt this system was began to be clear in the late 1700s and the early 1800s, leading to the first colonial revolts (including the founding of the US) and the end of slavery. The 2nd industrial revoluton, which allows civilization without slavery or servitude, and also allows modern warfare, began to bring an end to the era of classic colonial exploitation. It was replaced by a different exploitation more shaped by economic interests.