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Tear Jerker: A Boy and His Blob
The end of the A Boy and His Blob Wii remake has that scene where the character is dead, and the protagonist cries for a few seconds, and then the character is alive again except this time the blob turns into some unbelievably powerful robot immediately afterward and you think that's the end of it, until the surprisingly bittersweet ending where the blob returns to its planet leaving the boy's dark silhouette to gaze up at the moon, alone. Took me by surprise.