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I'm currently reading The Cost of Honor by Sally Malcolm, one of the Fandemonium published novels based on Stargate SG-1. Several times in the narrative, Col. Jack O'Neill's internal voice reminds him of a time when he killed Major Samantha Carter (allegedly "To save her").
It's been a few years since I watched SG-1 and I can't remember that happening. What is the book referring to?
It sounds like this is a reference to SG1: Entity. Sam was taken over by a space-virus thingy and Jack zats her twice (something that should otherwise kill her) to stop her from damaging the facility.
Possibly 4.20 'Entity'. An alien consciousness takes over Sam's body; O'Neill shoots her twice. No detectable brain activity, but they manage to restore her mind from a computer.
