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He doesn't, at least not permanently. He appears to be shot in "Day of the Moon", he appears to be drowned in "Curse of the Black Spot", he appears to be left in the Tardis for years and finally dying after years and years loneliness, his desicated corpse lying in a hallway adorned by the repeated words scribbled on the walls: HURT AMY KILL AMY. He then nearly gets killed by the Silence in "The Wedding of River Song"."