A Case of Conscience by James Blish is, on the surface, a novel about a crisis of faith when a priest is confronted with a perfectly moral and ethical alien society that has no sense of faith, or doubt or even guile. But James Blish is one of the most intelligent science fiction authors I've ever read, so the novel is also much more than that. Blish was an atheist for most of his writing career, or as Greg Bear mentions in the introduction to the version I read, an "apparent agnostic". Since he has written a Hugo-winning masterwork of religious science fiction, I'm leaning toward the agnosticism angle myself.
I've had little to no contact with the Society of Jesus, despite my lifetime immersed in Roman Catholicism. But from all I've heard and read, the Jesuits seem like my kind of Catholics, not afraid to wrestle with thorny problems of faith. Blish's Father Ramon Ruiz-Sanchez is not exception in A Case of Conscience. The book opens with the padre working his way through a labyrinthine moral dilemma in Finnegan's Wake, and we then find out he's doing this in his spare time, since he is actually a xenobiologist on Lithia, an alien world 50 light years from Earth. So Fr. Ramon is a man who has no trouble reconciling science and faith, since he places faith as a higher order of magnitude in his world. The crisis of faith comes to him subtly. His role on this planet is to determine its viability for human colonization. The padre doesn't do this through a purely scientific criterion. First and foremost he feels that it is necessary to determine the sentient alien species state of grace. They are called Snakes and their society has no deviants, no taboos, no restrictions of any kind, and runs like a precision instrument. As I mentioned before, their complete lack of philosophical and moral thoughts creeps Fr. Ramon out. When he finds out how the Lithians reproduce and raise their young, he falls close to the heresy of Manicheaism which is something along the lines of believing that Satan has creative power; or more broadly, in a dualistic universe. In my understanding, this is considered heresy because Satan is defined by absence and opposition, he refuses to be anything that God is, and therefore cannot be creative, he can only spin illusion, or somesuch. Needless to say, it is explained sufficiently in the book.
He comes back to Earth with a gift from the Lithians, one of their children. As Egtverchi grows up he becomes quite frightening, reminiscent of Ivan Karamazov, but even more nihilistic and dangerous. I think Blish intended this marooned being to be as close to Satan incarnate as he could get. The reader gets hit with a big old guilt-hammer here since we know that the only reason Egtvertchi thinks in the way he does, is because of the mistakes his caretakers made in raising him. I guess that makes his claims of ultimate free agency all the more frightening. Once a genetically predisposed rational materialist gets a bit of philosophy, look out! Not even the existentialists took their idea of freedom in such a selfish light.
I read this book in an evening, it is about 250 pages, and very interesting. Blish is a lot like C.S. Lewis, I think. A very intelligent man working his way through his own crisis of faith, his own case of conscience, for personal reasons. I get the sense that Blish was wrestling with these issues merely because they are always going to be there to be wrestled with and since he isn't bound to either of the dual sides he picks, he can make each of them equally potent. He'd've made a good Jesuit.
A tangentially related link: a few thousand science fiction magazine covers.
If you'd like more science as your religion instead of religion as your science, I recommend James Blish's Cities in Flight