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During the perfect ending, when the President says "Even though we tried to destroy him, he still saved us." after the comet is destroyed. And many responsible for the original attack on the station join in with many a My God, What Have I Done? lines to go around.
The slightly hero- Dark ending. Unlike the other endings where he ends up killing Eggman, he tells him to leave the sacred ark and never return, swearing to guard the place that was his home as long as he lives.
Shadow's dialogue with Maria in Lost Impact and The Doom.