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She sacrificed herself by jamming a closing door so that Bravo Marine could escape. She left behind data intel for Marine to pick up that would expose UAC's unethical experiments.
Sam's crushed remains ("SAM's remnants") were teleported back into hell back in Abaddon, where they were recovered by Stan Blazkowicz, O' Riley or Major Morgan. Sam's Remains are the last secret to find in Doom II RPG.