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The Baby refers to the name Samus gave the infant Metroid she witnessed hatch in Metroid II and decided not to kill, of which she became totally obsessed with in Metroid Other M due to feeling responsible for it's death at the hands of Mother Brain in Super Metroid. The joke itself refers to Other M portraying Samus as a whiny, menopausal weakling with a maternal obsession for a young parasite, completely betraying the stoic and dexterous roots of the character, which Matt, Pat and Woolie take major offense to.