We have to first mention the 'replay' function of the game. After clearing a area, most of the time you'll have the option of viewing through the event as it happened, meaning no slow motion and showing just how much of a unstoppable force The Dragon is to the outside view.
The Dragon's chase of V. Riding a motorcycle after him, he proves to be just as much of a menace as he is on foot, and when you finally get to V, you knock him off...and find he manages to board a attack helicopter, which he then proceeds to pilot. Once it's shot down, someone shows up, deeming himself the true Dragon as V brags about killing several NULL, before promptly slicing the latter's arm off, which is enough for The Dragon to retreat.
There's also a lot to love with the Hannibal Lecture The Dragon gives to V, before the car-chase happens.
Fifteen's rampage through the Prison. It's the only level where you play someone other than the Dragon, and he shows himself to be much, much more powerful than Zero ever could; being capable of performing a Flash Step so fast he effectively teleports, dodging rows of lasers Zero simply can't go through, and slicing any unfortunate foe in his path.
The Secret Boss. Not only is it extremely challenging and epic, but it manages to be one for both sides. The Body Horror combined with the general Creepy Awesome tone of the fight is one thing, but especially the opening. Like normal, Zero enters the office to kill his therapist. Unlike the normal ending, however, when Zero attacks, the therapist performs an effortless Punch Catch, doses himself with combat drugs, and takes Zero on personally.
The Therapist: I should have done this a long time ago.