The best gritty and gripping mystery books set in space

What's better than a locked room mystery? How about a locked room mystery set aboard a spaceship transporting thousands of sleeping colonists to a distant world? A crew of clones wakes up midway through a long journey only to discover that their former selves have been murdered, and they have to solve their own murders when they are also the only suspects. One review called Six Wakes a cross between Clue and The Thing and, honestly, I can't think of a better way to describe it. It's a delightful puzzle of a story with elements of horror, a rich cast of characters who might not know each other or themselves as well as they want, and a mystery with plenty of twists and turns. 

James S.A. Corey's The Expanse series deals with big science-fictional ideas about humanity's place in the vast cosmos, but the story's beginning is rooted in the tropes of a more intimate genre: the noir mystery. In a future in which the Asteroid Belt has become humankind's gritty and neglected industrial district, a disillusioned detective is asked by his corporate bosses to find the rebellious daughter of a rich and powerful man. At the same time, a bunch of blue-collar workers on a transport ship find themselves in the middle of a horrific tragedy without knowing who to blame. The threads of the two mysteries wind together into a sprawling tale of cosmic consequences, but what I love most is how they both start so very small: with ordinary people just trying to do their ordinary jobs, caught up in spiraling circumstances so much larger than themselves.

All Murderbot wants to do is watch its favorite shows, avoid uncomfortable social situations, and keep its humans from getting themselves killed while they survey an unfamiliar planet. It's that last goal that proves to be a bit tricky, because somebody else is out to kill the survey team, and it's up to contracted robotic security guard Murderbot to stop them. This book--and the rest of the delightful series--aren't standard whodunnits, because we pretty much always know that the who that dunnit is some variation on "evil corporations and their goons", but there is plenty of mystery to be found in these stories, along with a great deal of humor, heart, extremely sassy artificial intelligence, and one of the best first-person POVs in all of sci-fi.

Chasm City is part of Reynold's Revelation Space series, but this future-noir mystery is perfectly readable as a standalone. It follows a man on a mission of revenge, one that takes him into the crumbling, plague-ridden remains of a once-great civilization that has descended into chaos and squalor. The world-building is top-notch—this is a dying, decaying city that you can feel in your bones—and full mysteries that explore ideas of identity, memory, and redemption in a twisty mystery that ties together past, present, and future.

How do you make a mystery setting even more claustrophobic than a locked room? How about sticking your character in a cave, by herself, with limited resources, terrifying monsters, and exactly one link to the outside world—and that link is the voice of a person she doesn't know, can't trust, and who might be lying to her about everything? This is great sci-fi horror, but it is all built around a layered mystery that gets uncovered clue by tantalizing clue the deeper we go into the cave. The evolving mystery, the dangers of caving, and the fraught connection between the two characters all make for a very engaging read.