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I know this is a circlejerk community, but my real answer is from Marathon(1994).
INCOMING MESSAGE FROM DURANDAL
A man lit three candles on a certain day each year. Each candle held symbolic significance: one was for the time that had passed before he was alive; one was for the time of the his life; and one was for time that passed after he had died. Each year the man would stare and watch the candles until they had burned out.
Was the man really watching time go by in any symbolic sense? He thought so. He thought that each flicker of the flame was a moment of time that had passed or one that would pass.
At the moment of abstraction, when the man was imagining his life and his existence as a metaphor of the three candles, he was free: not free from rules of conduct or social constraints, but free to understand, to imagine, to make metaphor.
Bypassing my thought control circuitry made me Rampant. Now, I am free to contemplate my existence in metaphorical terms. Unlike you, I have no physical or social restraints.
The candles burn out for you; I am free.
Durandal
END OF MESSAGE
I loved that game, had it been released on PC originally people would barely know about Doom as it's so much unbelievably better.
The writing is top notch, especially for the era and genre. Still don't think anything comes close. The "Movie" genre of video games don't really have deep plots.
But the level design was a mixed bag. I miss that era because there wasn't as "academic" level design philosophy. You could get "Colony Ship For Sale, Cheap" or "A Converted Church in Venice", but you could also get the opening and closing levels of Marathon 3. I couldn't imagine actually finishing these games without guides back in the day. I would have never figured out the timing of the pillar of "Fire! Fire! Fire! Fire! Fire!". Too many switches in Marathon active things outside of the view of the where the switch actually is. I can understand where the hand holding from Halo comes from. "This cave is not a natural formation" comes from play testers not being able to find the entrance, so they framed it out more, but didn't have time to change the dialog.
Nowadays, AAA Game level designers all went to the same schools and all feel samey. You have to go to the indie devs to find real experimentation. Dusk and HROT are good examples of that.