Salera's Storm by J. R. Marro
For thousands of years, life on the planet Salera was peaceful...until the unthinkable happened. One of her own, Vorkis, sprayed a lethal virus into the atmosphere killing all the inhabitants except one, his cousin, Kalin. Vorkis flees and Kalin finds him deep within the core of Earth dredging for the most powerful source of energy in the galaxy, Pril. On the surface, violent earthquakes and real acid rain has taken the lives of millions. A strong-willed geophysicist, Rina Young, stumbles upon the plan of General Theodore Bauman: amplify the planet's weakened condition by igniting hundreds of nuclear warheads within the deepest crack in the Earth's crust, thus annihilating the unwanted and starting again with selective reproduction. But before she can warn anyone, she's caught by Bauman and sent tumbling in a mini-sub into the farthest depths of the ocean, on a collision course with nukes that are ready to explode, carnivorous creatures, a psychotic alien, and his cousin-dead-set on revenge.