More Tropes:
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Former Teen Rebel: (because Jess implies that she'll quit her stealing if she survives)
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Chekov's Skill: Jess stealing the canister from Yoder
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Bittersweet Ending: If you choose to save the Embryos
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The Dreaded: the troodon, and probably Dodgson(
"Is Dodgson gonna kill me?")
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Fridge Brilliance: the "easter eggs" usually count IF they're expanded to become relevant to the plot somehow