System Shock 1:
-Placing a C4 charge on one of the antennas, turning around only to see you're trapped by a forcefield.
"Make yourself comfortable, hacker. Stay a while."
...and then working feverishly when juiced up with drugs in order to OPEN THE DAMN THING BEFORE THE CHARGE BLOWS!!!
System Shock 2:
-encountering the Midwife Cyborg for the first time. Then finding Nurse Bloom's logfile on it...
"The genetic sequence he specified for the prototype...it's mine..."
-The Polito revelation, of course. "I AM SHODAN!"
-Getting jumped on by a hybrid yelling "Run! RUN!". I turned around, saw the thing charging me with shotgun...nearly had a heart attack.
-Getting into the cargo hold where Delacroix was supposed to be, only to find her dead...
Planescape: Torment:
-encountering your three previous significant incarnations and learning what a sick bastard you were
-the entire encounter with your own mortality
[hated the ending, though. there was simply no point, no explanation, no epilogue to it]
-"What can change the nature of man?"
Homeworld:
-The firebombing of Karak. I promised the bastards would pay in blood for every single dead Kushan. Recovering the cryo pads, with Fleet Command calmly reading out "One hundred thousand colonists secure...two hundred..." in a serene voice was also incredible.
-The last mission, seeing my giant fleet advance upon the Emperor's flagship. And the ending. The ending was insanely good. Everything played perfectly with the rest of the game, right down to the music in the ending credits. You don't see something like this much.
Homeworld: Cataclysm:
-"Who will remember the crew of this ship? Or are flicker-lives not worth remembering? You are WORSE than the Beast! At least the Beast doesn't PRETEND to be righteous!"
-The ambush mission, with the Khar-Selim showing up at the last minute
"And we brought friends!"
-The ending. Marvelous. You may say whatever you want about Cataclysm, but they did the ending well.
Shogun: Total War
-Repealing wave after wave of enemy attack with just 240 troops, and at the end of the battle, seeing the enemy Daimyo fall down from his horse while he was cowardly running for his life. He nearly made it, too. He died right at the edge of the archers' range
-Many a glorious victory against overwhelming odds
Red Faction:
-I disabled the nuke at the end with precisely ONE FUCKING SECOND LEFT. You can't even begin to imagine how I've felt after seeing that goddamned counter stop
It was SO holywoodish.
Fallout:
-The ending. The rest of the game rocked, but the ending was incredible. Short and to the point, tying well with what preceded it.
I-War
-Every cutscene. There were no better ones in any of the games i've played to date.
-The mission where your ship gets boarded by a pirate, and you strike a deal with him...revealing a hidden cache of loot you've mined beforehand
-The ending when you remain loyal to SecPat, and follow the President's cruiser.
"We have to end it. Right now."
X-Wing:Alliance:
-Hypering into and area to get your sister out from a mining station, and seeing THE FUCKING EXECUTOR leading the attack. Getting out of there from under the Imperial nose was also a treat....of course, later on I realized that you could kill the Executor with the Otana, and the entire moment got cheapened immensely
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I could go on like that forever. Ah, memories, memories...