well spiritual/religious level isn't really my thing, so I guess I'd say the game that probably hit me the most emotionally was probably that famous moment in FF7 since I'd never played an RPG before where a main character had died like that. Those kind of moments always get me like the similar one in VC.
Other than that the patriotic ending of MGS3 really got to me too as an army brat. Moments of self-sacrifice particularly when you know you'll be hated for it in the end are some of the most beautiful stories in my opinion.
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