The Sparrow, by Mary Doria Russell.
There are plenty of great first-contact hard science fiction stories. But The Sparrow contains a number of aspects that set it apart from other works. The fact that the first contact appears on their planet is a change of pace, as is the makeup of the crew , and the time spent on the crew's spirituality and spiritual response to the experience. There is even a sprinkle of courtroom drama.
Emilio Sanchez is part of a crew sent to explore a new planet, a crew financed by the Jesuit order. He ends up being the last survivor of the crew, and the state in which he is discovered when a rescue ship from Earth arrives brings shame and disgrace to Sanchez. His physical injuries are just one part of the trauma he has gone through, bringing harm to his body, soul, and spirit. Most of the crew is found dead, and Sanchez himself is found in a compromising situation, accused of (and also the victim of) heinous acts.
Alternating between a range of time frames, Russell is equally compelling in telling the stories of Sanchez's early life and ministry, of the actual events of the crew of the mission on the alien world, and of the investigation by the Jesuits into Sanchez's acts on the planet. The suspense that this structure builds adds great tension to the book.
I was nervous heading through the last chapter, as it seemed that the clichè of "spiritual person loses faith as a result of trauma" was coming, but even this plot point did not go down the predictable path.
This novel is a great read, a throwback to the thought-provoking stories from the early days of hard science fiction.