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Melody Pond (later known as River Song) was kidnapped because she was conceived in the TARDIS while travelling through the spacetime vortex. That gave her some of the characteristics of a Time Lord, although her parents, Amy & Rory, were both human. A faction of the Silence wanted to enhance her Time Lord characteristics so they could use her as a weapon against the Doctor. This was explained in "A Good Man Goes to War", although it was never made clear just why that faction of the Silence thought Time Lord characteristics were needed by their weapon. They were successful in enhancing those characteristics but only partly successful in conditioning her to be a weapon. (In "The Wedding of River Song", for example, she managed to resist the conditioning.)

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