User blog comment:IceFireWarden0/Speculations for Season 11/@comment-3231264-20121124061051/@comment-4148373-20121212004622

The Huragok "fixed" Alpha, by removing whatever was causing him pain. At least, from what I can tell that's what it did. Not break him. I don't know the "removing cause of pain" part, but the Director told it to "fix" Alpha, and to "remove everything that is broken", then put it into a storage device. So I would guess that the AI fragments are whatever aspect was causing Alpha pain during his torture. In Episilon's case, it was memories, mostly his memories of Tex. Since this is only one we actually see the torture for, I can't say for certain, but I can think of ways to separate most of the AI, if my theory is correct. Something that can't be logically solved, for Delta, some form of betrayal for Theta, a secret he kept causing a disaster for Gamma, a situation where his anger caused him to fail for Omega, the list goes on. Though Sigma, being 2 different emotions, would be tricky.