I was just thinking about the little touches I love about this game, the things that aren't really overtly stated or shown, but they're just presented so well.
Like at the end of the game after the EVA escort mission and you reach the lake, and Naked Snake just sort of turns and looks at the flower field. Then EVA turns and sees him, and he looks back at her. It's difficult to describe with just words, but just the emotion that's displayed without either of them saying anything is great. The stuff between Naked Snake and The Boss is just so emotionally charged. I love it.
MGS3's presentation is just so good in general. I love the part right after The Sorrow "fight" where Snake washes ashore in the forest, and he rises up on his knees and the camera just slowly pans back to show the forest.
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"Stay with me until the end. Please."
"Not until the end. Always."