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Possible dialogue choices at two points of the story are "It's time to kick @$$ and chew bubble gum. And I'm all outta gum." and "I came here to chew gum and kick ass, and I'm all out of gum."

These are references to Duke Nukem's catchphrase, and in turn, the 1988 film They Live.
Contributed by DeerBoarDude
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The "Spine Reticulate" upgrade for the Shield Booster room, along with the mention of city production in its description, are references to the SimCity series and its recurring gag involving "Reticulating Spines".
Contributed by DeerBoarDude