The level where you have to trigger several gas taps throughout a building to fill the whole thing with gas. You then drop a broken transformer on top of the whole thing. The build-up and the payoff are nothing short of satisfying.
The Marked Ninja standing against Azai after dealing with the Hessian Services. He refuses to commit suicide and escapes from a room full of people trying to stop him with a simple smoke bomb.
Perhaps not for the Marked Ninja, but one for Azai. After realizing his star pupil has fallen to madness, not only does he keep his calm after the marked ninja returns and finds his way to the inner garden, but he doesn't even bother to fight the marked ninja, inviting him inside, giving him a sword, and then kneeling there to let the marked ninja make his own decision, and doesn't even show a single sign of fear during the whole encounter.