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In the recreation room when examining the poster of billiard balls Sigma will say, "What's this supposed to be a picture of?" to which Alice replies, "They're those balls from that kid's show, right? If you collect seven of them then you get a wish." This is a reference to the series Dragon Ball.
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When going through the control room, a set of boxes can examined. Luna will then tell the player that they contain machinery. Examining them several times will cause Phi to wonder if they could "use one of those boxes to sneak past guards." This is a reference to the famous cardboard box item in the Metal Gear Solid games.
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In the Vita version, two trophies begin with the phrase "Who Set Up Us The Bomb". This phrase is a direct-reference to the videogame Zero Wing where a mechanic is seen in the opening of this game saying "Somebody set up us the bomb."
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