What remains of the Enlightenment is collapsing for structural reasons. This discourse doesn't reat upon political or academic theories, nut upon facts and direct observations. Obviously I'm simplifying (one can't write history any other way), but minus the inevitable exceptions and complications, this is what has happened and what is happening.

How The Enlightenment Gained A Structure
The Enlightenment began with a collection of outsiders studying science. They had little backing and few credentials. In fact, the motto of the first group (that became The Royal Society) was Nullius in verba: "Take nobody's word for it." There was a lot to like in the early Enlightenment, and it led to a long string of crucial discoveries.

Halfway through its run, however, at about 1750 AD, the Enlightenment took a dark turn. Rather than working to discover what was right, it began to fixate on what was wrong. That is, the leading voices of the Enlightenment left off building and moved into tearing things down.

That change ran the late Enlightenment directly into the French Revolution, but we'll pass over those details. You can find more in our Free-Man's Perspective issue entitled Darkness From The Enlightenment.

Bear in mind that there hadn't been a large intelligentsia in Europe before this time. While the Church did have an intelligentsia, it wasn't expansive, and the Protestant Reformation had recently broken the Church's monopoly on supplying rulers with bureaucrats, lawyers and advisors. 

And so a new intellectual class began to form and soon enough began seeking power. But since they saw no way to take power from monarchs, they turned to the Church and began plundering its legitimacy. If they could become the new arbiters of reason and truth, they'd have the same kind of power the Church had enjoyed.

And so the new intelligentsia went about to seize the legitimacy of the Catholic church, bringing it to themselves. As historian Margaret C. Jacob wrote:

They removed God and in his place inserted the blind forces of matter in motion.

These new intellectuals (especially in Protestant areas where attacking the Church was appreciated) were given positions in the universities that had sprung up several centuries earlier. The universities were, by this time, mainly under the control of secular rulers.