It's often said that a mystery is a story about solving a crime while a thriller is one about stopping a crime. I don't necessarily agree with that definition of thrillers, though I know it is widely used. Thrillers plots are not all about stopping a crime. I think, however, there is an element of mystery in all thrillers—not necessarily a criminal act, but some mysterious initiating action that must be pursued to understand it.
In my sci-fi thriller, Eden, for instance, the mystery surrounds the discovery by trapped American GIs of a futuristic esophagus in the ruins of an ancient temple in war-torn Iraq. In my latest novel, Polar Melt, the mystery involves an anomalous energy source at the bottom of the Arctic Ocean.
When it comes to mystery thrillers, however, I think the key components (mystery and thriller) can be parsed. The mystery usually—but not always—involves a crime and the attempt by the protagonist(s) to solve that mystery. The plot can be character driven as in cozies and whodunits and, to some extent, hard-boiled mysteries, or it can be driven by procedure, as in police procedurals.
Thrillers plots are driven by a need to create a suspenseful atmosphere by adding elements of action and danger. Whether they be mystery thrillers, action thrillers, political thrillers, sci-fi thrillers, it is the action or suspense that pushes the plot forward.
David Morrell's novel, First Blood, is credited with creating the modern thriller genre. It is a classic action thriller. There is no crime to investigate, no politics, no sci-fi elements. It is the story of two men involved in a violent struggle against each other. An abundance of action and strong characters drive the plot forward.
On the other hand, Lawrence Block's A Walk Among the Tombstones is pure mystery. There are no gunshots, no fistfights, no car chases in the whole book. The plot is driven forward by Block's powerful characters, particularly his protagonist, PI Matt Scudder. Anyone who dies in the novel, dies offstage.
My first novel, The Killing Depths, a mystery thriller that takes place aboard an American submarine, has occasionally been compared to Tom Clancy's The Hunt for Red October. Both take place on submarines and both are full of undersea combat. Hunt, however, is a military thriller; the plot is driven forward by military technology and the undersea hunt for the Soviet submarine Red October.
The Killing Depths does have aspects of the military thriller in that two opposing submarines are in a struggle to the death. But the main plot is a murder mystery involving the slaying of a female crew member and the protagonist's search for what turns out to be a serial killer. The submarine conflict alone would be a thriller plot. The search for the serial killer alone would just be a mystery plot. Blend the two and you have a mystery thriller.
My latest Linus Schag novel, The Butcher's Bill, a sequel to The Killing Depths, involves an NCIS agent's investigation into $9 billion in cash that disappeared from Iraq during the American war there. That alone is a mystery plot. Make that character a rogue agent who appears to go on a killing spree, toss in some corporate mercenaries out to silence him, and you have a mystery thriller.
So, in its simplest form, the mystery thriller—unlike the generic mystery and generic thriller—has a plot driven forward by both the discovery of clues and the action or danger leading to their discovery.