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At the time, Aperture Science and Black Mesa were having a race over portal technology. The Black Mesa incident opened a giant portal connecting Earth and Xen.

My theory is that GLaDOS thought that Aperture Science was inferior, comparing to what Black Mesa did, even though it was just an incident. So GLaDOS shut down the facility so that the scientists had to work day and night to catch up with Black Mesa. Is this true?

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I know that the two franchises share the same universe, but what are you basing this idea that GLaDOS thought Aperture Science was inferior on? – phantom42 Nov 2 '12 at 14:26
There's quite a bit of in-game literature indicating that Aperture was frequently Runner-Up "US Department of Defense's Contractor of the Year", I can't recall if it's expressly stated or just heavily implied that they lost to Black Mesa. – Brandorf Nov 2 '12 at 15:00
@phantom42 Valve releases a lot of extra media, comics, updates, and stories I believe that tie into it's portal/half-life universe. This is definitely a constructive question. – AncientSwordRage Nov 2 '12 at 18:21
Well, GLaDOS does seem to hate Black Mesa. – Anthony Arnold Nov 5 '12 at 4:50

GLaDOS was created because Apeture was behind on Black Mesa, it was the final challenge to create the superior Disk Operating System. GLaDOS was designed specifically to be victorious against the Black Mesa contract so then it is unlikely that she had any respect for her rival.

Furthermore, we know she was turned on on Bring your daughter to work day, and almost instantly attacked. Although it seems that they attempted to wrestle control from her, and even were successful at one point (long enough to set up a phone and a morality core), in all likelihood the events occurred far to quickly, and GLaDOS knows little about Black Mesa then what was in her computer banks or was known by Catherine.

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Let X = "defeat Black Mesa" and Y = "don't kill Aperture Science scientists". Both objectives sound perfectly acceptable. Given that GLaDOS didn't do Y, what guarantees GLaDOS would do X? Just asking, I don't remember well the game anyway. – Voldemort Dec 5 '12 at 6:13
@Omega: Is there any proof that Y is a command? GLaDOS is crazy and doesn't value human life as relevant. Anything can happen at that point. – MPelletier Dec 5 '12 at 13:18
@MPelletier: Y is an objective that derives from X. To defeat Black Mesa implies to support Aperture Science. You don't support Aperture Science by killing the scientists - even though GLaDOS was self-sufficient, killing the allies can only be harmful for her main objective (thus unnecessary/illogical). Allies can only help. – Voldemort Dec 5 '12 at 16:21
@Omega It makes sense to us because we're human. GLaDOS would gladly counter that argument with nerve gas. Actually, GLaDOS has pretty much the ethics of Cave Johnson, who didn't see safety as very useful. Take it a step further, if GLaDOS sees that the scientists are a possible cause of errors, then killing the scientists produces less errors. – MPelletier Dec 5 '12 at 19:14

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