Man, talking about the twist in 'Killer Elite' gets tricky because it depends on which one you mean! There's the Robert Ludlum novel and the movie adaptation 'Killer Elite' (2011) which was loosely based on a different book, 'The Feather Men'. Assuming you're asking about the Ludlum book, the big pivot isn't a single 'gotcha' moment so much as a gradual reveal of the true enemy. You spend the whole book thinking Danny and Sam are up against this ruthless mercenary organization, Obsidian, and that it's a straightforward revenge/rescue mission.
But the real gut-punch is realizing that the manipulation goes way deeper, right into the halls of power they thought were safe. The client who hired them, the very agency or government element seeking justice, is often compromised or is actually using them as pawns in a bigger, dirtier game. The twist is the erosion of trust; the enemy isn't just the obvious assassin, it's the system that created him and is now trying to clean up the mess by eliminating its own tools, including your protagonists. It turns a personal vendetta into a profoundly cynical political thriller where the only way out might be to beat both sides at their own game, which Sam and Danny reluctantly have to do.
Ludlum loved that theme—the paranoia of not knowing who to trust—and here it plays out through action set-pieces and sudden betrayals that reframe every previous alliance.