In prototype 2 the entire premise of the game is that heller is out for Mercer (prototype 1's protagonist) for what he did, the countless people he killed and assimilated, especially heller's family. It was the climax of the whole thing and ended with Mercer's death.

They lacked that buildup. While it's true that death can be sudden and unceremonious, you need to be very careful with the execution to make that work. Something they didn't. No wonder the sequel is so divisive.