User blog comment:IceFireWarden0/Speculations for Season 11/@comment-3231264-20121124061051/@comment-4616231-20121212015838

They apparently have the Alpha go through a scenario that would cause it's mind to fragment off an emotion. Or some shit like that. Then, seeing as it's a fragment, they just have to have the Engineer move it from Alpha to somewhere else. Because this is totally how technology works.

If that's the case, then the torture scenario we saw was fragmenting Memory. Which was actually pretty lame, because all Director had to do was go "TEX DIED LOL". Apparently Alpha couldn't accept this, and purged the memories of it. Basically he was in denial.