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GLaDOS is different in Portal 2 because she is in another body. We know there are multiple GLaDOS chassis because in the comic there are multiple GLaDOS prototypes and in the games she activates multiple cores, is put in to the POTaTOS body and tells the robots P-Body and ATLAS that there is an intruder in one of her old chassis and forces them to confront it. However her new body is and old prototype and has very limited power over the facility and in the multiplayer function the robots put discs into the GLaDOS mainframe and restore her to full power. The way the prototype body got down to the GLaDOS control room is decaying walls and floors that crumble over the decades allowing the body to drop in.

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Q: Why does GLaDOS have a different head in portal 2?
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