Aya getting up and shooting Hyde at the last moment. Hearing her much more self-assured voice along with her Big Damn Heroes save made the whole game worth it for this Troper.
Speaking of the bastard, the two boss battles against him are a stand-out showdown. First being in a skating rink. Unfortunately Hyde overwhelms Aya but not until her deceased allies come to save her by sacrificing their vessels. And finally, the last battle against him. Aya in her ultimate phase against Neo Hyde Bohr. Two souls, both in their strongest forms duel it out in a piece of land in the middle of subspace, fighting only for one purpose: the truth behind Time Zero. To make things even more awesome, the music... Dear God,the music!
For most of the game, we've seen even the most elite soldiers on the planet slaughtered by the Twisted. In the final stage, what remains of the Coalition forces are scattered, leaderless troops, trapped in the enemy's base, just trying to go out fighting. They form up into organized units, work together and they kick ass.
In Operation Red Fog, you get on a stopped subway train which then starts moving and a bunch of Twisted come out. Then two Delta Force troops jump onto the moving train to give you some backup.