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Valve probably killed Eli off to give further explanation and to motivate the story of Episode 3, but this is just speculation, no one really knows why Valve killed Eli off. It may have also been to further the recently-revealed relationships G-Man has with other characters, seeing that Gordan and Alyx have both been saved on a few occasions by him, while here we see Eli, another contact, no longer under his protection.

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