The Rising Tide — J. Scott Coatsworth

Earth is dead. Five years later, the remnants of humanity travel through the stars inside Forever: a living, ever-evolving, self-contained generation ship. When Eddy Tremaine and Andy Hammond find a hidden world-within-a-world under the mountains, the discovery triggers a chain of events that could fundamentally alter or extinguish life as they know it, culminate in the takeover of the world mind, and end free will for humankind. Eddy, Andy, and a handful of other unlikely heroes -- people of every race and identity, and some who aren't even human -- must find the courage and ingenuity to stand against the rising tide. Otherwise they might be living through the end days of human history.