What phases of baroque are tied to religion and how?

What is typical of artists labeled Baroque is the emotionalism and extravagance of their color and design. This ties into religion perhaps paradoxically because sensuous imagery could have been thought disrespectful or even blasphemous in an earlier time. The result of both the Protestant Reformation and the secular humanist trends of the 1500s and 1600s changed what artists and intellectuals regarded as appropriate forms of expression. To some commentators, the baroque has been considered a part of the counter-Reformation to restore the hegemony of the Roman Catholic church, but this is a simplistic way of looking at it. Artists in general began to appeal more directly to the emotions. The religious paintings of Rubens, for example, infuse a sexual energy into their subjects in a way that would have been considered improper in an earlier age.
What we see in the Baroque is a kind of sensual propagandizing for religion. Artists realized that the visceral, emotional appeal of a work is often more important than intellectual qualities or the purity and elegance of line so prized by the Renaissance painters.
A few examples might be in order. Caravaggio's "Judith Beheading Holofernes" and "The Crucifixion of St. Peter" are typical of a new boldness, a raw, unadulterated expression that seems to revel in violence and pain. It is a new, unimpeded, and immediate way of expressing religious faith. The same is true of works by Rubens such as "Samson and Delilah" and "Daniel in the Lion's Den." There is no distinction between the explicitness, the showing of naked, amply fleshed figures in these religious paintings and the same style in the depiction of pagan, mythological subjects, as in Rubens's "Prometheus Bound," among many others.
Ironically the new approach to religious art may have been partly a result of the changing, and increasingly secular, view of the value of earthly life and the increasing tendency in intellectual life to question the established ways of doing things. In the Baroque, we see a foreshadowing of the emotionalism that was to pour forth even more freely in the Romantic movement 200 years later, after European thought had been decisively transformed by the Enlightenment.