Earth 2.1: Regenesis — William Crow Johnson

Exiled commando Major Alexander Khan must save not only a selected ten thousand from Earth's destruction at the hands of the alien Kurg. He must save his adopted planet from domination by power-mad Nathan Fox, dictator from Earth who allies himself with the genetically engineered Kurg to gain power over the new planet. Khan gets help from his half-alien daughter and the Nephilim, the human-appearing alien race who created the Kurg -- and who have circulated undetected among humans for tens of thousands of years, shaping our history. After the devastating conflict, the remnant populations must learn to live together -- ten million already on the former prison planet, the ten thousand refugees from Earth, the Nephilim, and the surviving but transformed Kurg -- and form one people.