Star Trek and religion have an interesting relationship.
Gene Rodenberry was proudly an atheist and believed that the future would result in people "outgrowing silly superstitions." Others in the franchise, like Ron Moore, made Deep Space Nine one long rebuttal to anti-religious science fiction.
Some authors have come in one one side or the other but few have tried to deal with the issue from a secular point of view. How does religion impact the lives of people who don't have miracles from the Bajoran prophets to justify their faith? What is the importance, if any, of religion when the deities they worship are confirmed as false?
Shockingly, this isn't just what Ex Machina tackles. It also discusses, in a somewhat off-hand manner, the nature of the Singularity. The Singularity, much like the Tao, cannot be described because both are entities which are indescribable by their very nature. The Singularity is when we reach a point technologically or socially we cease to be able to be understood by normal humans.
Christopher Bennett tackles the Singularity-like event of Star Trek: The Motion Picture and questions what this would mean for individuals seeking religious answers in the cosmos. In short, if you're looking for a god, what happens when a being is created who might as well be one? All of these questions and more get asked during the novels and answered with a somewhat reasonable extrapolation of facts.
The novel's premise is Captain James T. Kirk is still recovering from the events of TMP. Having witnessed William Decker sacrifice his life to become one with V'ger, he's left with a crew which (rightly or wrongly) blames him for their former Captain's death. Spock, meanwhile, is struggling with his recent decision to abandon the pursuit of pure logic to rediscover his long-suppressed Vulcan emotions.
James McCoy is regretting his decision to return to Starfleet. As a result, they are all eager to answer a distress call from a 'Hollow Earth' planet they destroyed the machine god of many years before. This happened in the 3rd season TOS episode, "For the World is Hollow and I Have Touched the Sky."
Once there, they find the planet is rocked with religious strife as the discovery their machine god was false has not gone over very well with the populace. Likewise, the former high priestess' attempt to indoctrinate them all into a modern secular worldview (we can even say atheist) has only made things worse.
Were this an episode of TOS, Kirk would resolve it by finding the terrorist leader and punching him or convincing everyone that they need to work together with a single speech. Things are a bit more complicated here and Christopher Bennett ties Kirk's cautious approach to events with his recent experiences. He even deconstructs Kirk's rather causal way of dismantling cultures as well as the crew's habit of having once-an-episode life-changing romances.
Part of what I enjoyed about this work is the "new" characters, only barely glimpsed in TMP. The crew of the Enterprise, meant to be the cast of Gene Rodenberry's Phase 2, includes many more aliens than we're used to. Rhaandites, Betelgeusians, and other ones barely glimpsed in the later canon. My favorite of the new crew members, however, was Reiko Onami. A woman who has spent her entire life around aliens, she finds "regular humans" like Doctor McCoy petty and bigoted.
I also was a huge fan of the contrasting characters of Natira and Rishala. Two high priestesses, they could not have more contrasting opinions. Natira embraces her new atheism and Federation agnosticism, feeling it has liberated her from a repressive evil religion. Rishala, however, holds to deep spiritual truths while expressing many of the Federation's highest virtues.
They are twin sides of the same coin but deadly enemies due to how differently their experience with their planet's religion shaped them. In-between them are many characters of varying beliefs, shaping the complicated narrative of the book.
In conclusion, Ex Machina is an excellent story. It's a bit more complicated than most TOS stories and a good deal more cerebral. However, this doesn't mean it's boring. Indeed, I found it incredibly engrossing. Deep characterization mixes with an in-depth analysis of an interesting subject. I recommend all fans of the original series as well as the movies.