Soil (The Last Flotilla Book 2) by Colin F. Barnes

Summary:
It has been almost three years since a mysterious natural disaster left the Earth submerged beneath the oceans, and still the sole survivors cling desperately to life aboard their flotilla. When they learn of a secret government facility located deep below the surface, an expedition party headed by Jim, the group leader, and Eva, a former cop, sets out in the hope of uncovering the truth about their drowned planet.

But when the ragtag submarine crew, riven by discord, united in distrust, finally arrives at the underground bunker, the scene that awaits them offers more questions than answers. What happened here to incite such shocking acts of violence? Who is responsible—and where are they now?

Jim and Eva are determined to follow the trail through to its dangerous end. But the farther they venture, the more sinister their world becomes. How high up does the conspiracy really go?