Alex Mercer should have been furious and downright frightened in the situation he was currently in.
James Heller—his favorite "child", a man who showed a lot of promise in the eyes of the viral god-general—had defeated him. Actually, "defeated" was putting it lightly. Mercer had been completely and utterly destroyed by his progeny, and was now left at his mercy. The hooded bioweapon was on his knees in a puddle of his own blood, which flowed out freely from his freshly severed arms.
Mercer could only look back on the events that led up to this moment. He thought he saw a kindred spirit in the former Marine sergeant, even though Heller hated the hooded bioweapon with every fiber of his being. Heller was a man who lost everything and had nothing else to lose because of it. His attitude reminded Mercer of himself—at least somewhat—when he was seeking his own revenge during the previous outbreak 14 months ago. That was why Mercer saw a potential second-in-command in the making; someone who was loyal to his cause, a constant companion in a world that despised him.
That was also why he was both furious with and disappointed in Heller's defiance. Why didn't Heller put his ruined past behind him and appreciate the second chance that Mercer had given him? Part of Mercer had hoped getting little Amaya involved would force her father to come around and repent for his misdeeds—although the hooded bioweapon was still primarily interested in the young girl's genetic potential—but a larger part of him just wanted to see his defiant "child" suffer. Heller would've lost the only thing he had left in his worthless life—the one thing he thought was taken from him—and he'd have no choice but to return to his new "father".
Despite all this, however, Mercer felt strangely satisfied. He now realized why he failed to consume Heller when he got the chance; it was also why he had been so soundly defeated. Heller's rebirth and still-growing powers represented a new, significant stage in the Blacklight Virus's evolution. This realization gave Mercer peace of mind; he gained renewed confidence that his new world would still come to fruition. Even if it didn't, death was better than being eternally surrounded by weak creatures who constantly feared him and his "children".
Mercer accepted his defeat with grace; he had done well to choose Heller after all. His one regret was that he couldn't see for himself what the ultimate pinnacle of the Blacklight Virus's evolution would look like.
With his fading strength, Mercer gave his congratulations to his favorite "child" for accomplishing what he thought was impossible.
"Welcome to the top of the food chain."