What is the conflict between religion and science in "The Star"?

The fundamental conflict between religion and science in
The Star lies in the central character.  The narrator straddles both worlds in his own
sense of being.  He is both a Jesuit priest and an astrophysicist, who believes that
scientific exploration can shed light to God's masterful plan in its intricate glory. 
The fact that he straddles both worlds, set up as opposing one another is something that
brings the conflict into light.  Both the public that the narrator serves as well as his
fellow crew members are both skeptical of religion, and it is on the shoulders of the
narrator to make the case that God is merciful and loving as well as the master
architect of a plan to love and respect all of mankind.  The conflict further deepens
with the revelation that the narrator has come to understand about the supernova.  The
resulting luminous star of Bethlehem has come at the cost of a civilization.  This
unsettles the narrator, whose scientific study has revealed some basic realities about
God that question his faith and his assertion about the divine being.  The fact that the
scientists discover that God wiped out a civilization to show preference to another is
unsettling.  The destruction wrought is incompatible with a merciful and loving God. 
The ending reveals that science has brought forth an understanding that undermines the
essence of religious and spiritual faith.  In this, the narrator represents the
fundamental conflict between religion and science.