The Envoy

A civilization of aliens called Homakuwa exists under the seas and has now chosen to reveal itself to the surface world. The world is in an era of unprecedented peace, due in part to a single government, the Unified World Government (UWG), and because a new Prophet has appeared with a message of tolerance and non-judgment. Rather than a conflict with existing religions, he has absorbed them into Faithism.
Plots against this new religion and the UWG turn into active conflict. The Homakuwa civilization, actually native to Earth, is caught in the middle, condemned and feared for their ability to genetically manipulate and create life as the surface civilization engineers and builds things. The alien civilization creates beings adaptable to the environment of outer space and expands into a number of habitats orbiting the Earth and on the moon. In the midst of the conflicts on Earth, an asteroid hurtles into the Solar System breaking up and heading toward Earth. Homakuwa and the surface dispatch interceptors to deflect the incoming meteoroids, but only the largest and most dangerous objects can be diverted.
A number of smaller meteorites strike the Earth resulting in Impact Winter, almost destroying civilization. The Collective mind of Homakuwa, the remaining surface world survivors, and the Prophet struggle to rebuild, while Homakuwa begins to expand their society. As they do so, they evolve into a new species.