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So in Episode Two the g-man talks about how, when he "plucked" Alyx Vance from Black Mesa, someone protested that he gain use of Alyx for his own purposes. One might think that it was Eli or Alyx's mother, Azian, that might be voicing these protests, but it has been noticed that when the g-man says this, it is Dr. Wallace Breen's portrait that appears on the screen behind the g-man.
So, here is my theory. After the resonance cascade occurs, Eli stays in the Anomolous Materials laboratory, at least for a little while, to attend to one of his colleges. He claims in Black Mesa East that he carried Alyx from Black Mesa himself. I think he was lying. I think that Eli's self-proffesed "oldest friend", Wallace was able to meet up with Eli's wife and daughter before Eli himself was. Or perhaps neither Eli nor Azian were able to get to Alyx and Wallace was able to find her in the day-care centre and take her himself. Either way the end result is the same: Wallace was the one carrying Alyx from Black Mesa, with or without Azian.
I think that Eli and Wallace's mutual friend appeared to him and he struck a deal. I think that Alyx and Breen were given safe passage from Black Mesa in exchange for Alyx's freedom. I think that Wallace tried to negotiate a better deal, but couldn't, and took what he was offered.
And if Eli knew about this, well, it was another reason for bad blood between him and Breen.
So, here is my theory. After the resonance cascade occurs, Eli stays in the Anomolous Materials laboratory, at least for a little while, to attend to one of his colleges. He claims in Black Mesa East that he carried Alyx from Black Mesa himself. I think he was lying. I think that Eli's self-proffesed "oldest friend", Wallace was able to meet up with Eli's wife and daughter before Eli himself was. Or perhaps neither Eli nor Azian were able to get to Alyx and Wallace was able to find her in the day-care centre and take her himself. Either way the end result is the same: Wallace was the one carrying Alyx from Black Mesa, with or without Azian.
I think that Eli and Wallace's mutual friend appeared to him and he struck a deal. I think that Alyx and Breen were given safe passage from Black Mesa in exchange for Alyx's freedom. I think that Wallace tried to negotiate a better deal, but couldn't, and took what he was offered.
And if Eli knew about this, well, it was another reason for bad blood between him and Breen.