Redemption / Mark Walden.

Enhanced descriptions from Syndetics:

Sam and his friends embark on one last mission, one final epic final battle against their alien enemies to determine the fate of the Earth in this fast-paced, action-packed conclusion to Mark Walden's Earthfall Trilogy.

After the death of his father, Sam is still struggling to come to terms with the Illuminate powers that he inherited, the changes that the alien nanites have wrought on his body, and the mysterious summons calling to him, urging him to come and retrieve "his birthright."

After separating himself from his friends, Sam realizes the call is coming from the Primarch, an ancient spaceship and the first of the Voidborn, a digitized Illuminate consciousness, that was driven insane after it was left drifting lost and alone in space for thousands of years. It's calling to him to join the fight and destroy the Vore.

But just as Sam thinks he finally has an ally against the Vore, he realizes the Primarch has an agenda all its own...

As the final conflict takes place in the skies above the Grand Canyon, Sam is forced to confront the fact that even with some surprising new allies, the price for defeating the Earth's invaders may be vastly more than he is prepared to pay. One thing is certain, whatever happens, life will never be the same for Sam--or for the rest of humanity--ever again.