Many describe Cameron’s actions in season 2 as having been the result of a persistent “glitch” (presumably one that’s fixable). Most seem to view it as a hardware problem. I’m still not sold on the idea that Cameron’s chip is necessarily glitchy. Since her CPU was damaged, there is no doubt that she’s been having to work through various conflicts that weren’t conflicts before.
Obviously there is the conflict of the emergence of the Allison persona. I don’t think that was ever supposed to be anything other than a template for her terminatory self to use when necessary, e.g. in “Pilot” when she’s being all flirty with John before Cromartie starts shooting the place up. In “Samson and Delilah” (S&D), I think her desperate accessing of it to try to keep John from pulling her CPU started this cascade of conflicts.
What the S&D accessing did was essentially force a cyborgy type of DID (dissociative identity disorder) on Cameron. “Allison From Palmdale” saw the full-on manifestation of this as she went all “Sybil” and became a totally new person with no memory of her other, primary, personality. It wasn’t until John reminded her that she was a machine from the future did that dominant personality start to reassert itself.
Since that time, Cameron has had to essentially become her own psychologist, trying to get her personalities to reconcile. While the terminator one remains dominant, the secondary Allison persona continues to want its voice heard. This was clearly manifested in “Ourselves Alone” when the bird suffered from “an involuntary movement of my fingers”.
Despite an attempt to fix existing problems in Cameron’s endoskelton, Cameron continues to experience “an involuntary movement of my fingers” during certain very specific situations: when the terminator persona wants to enact a termination while, at the same time, the Allison persona is preventing it. The “glitch” that results in Cameron’s left hand spasming isn’t due to a hardware “glitch” but a psychological one.
Eventually, though, Cameron seems to have been able to find that necessary middle ground. We first notice this at the end of “Today is the Day, Part 2” when Cameron holds a pidgeon and appears to be confident that it will not experience a cyborg squeeze. This was not the case in “Today is the Day, Part 1” when a bird (apparently a potential one in a long line of test subjects) flew away causing Cameron to comment that there was “a fifty-one percent chance” that she wouldn’t have killed it.
Still, by “Born to Run”, Cameron has reached a point in her acceptance of the situation that she’s honest with John. She admits that fundamentally she’s built to kill him, and she might at some point. But she doesn’t. She implies that she doesn’t because now it is her choice not to. It might not always have been so.
I’ve suggested before that even if Cameron was reprogrammed by John, that there would still be a lot of fundamental code (probably self-healing code) he couldn’t touch and still have a working robot (essentially her BIOS). What may have happened is that pre-S&D Cameron was not killing John due to his reprogramming in the future. The injury done in the explosion basically voided John’s programming (“sometimes they go bad, no one knows why”), but the psychotic break in the effort to keep from getting her chip pulled resulted in a terminator that no longer need John’s hack to keep it from its fundamental mission.
Cameron may or may not be “whole” at least up until letting John Henry have her chip, but she was in control. She had reconciled much of the conflict between her two personalities. By the end of the second season each personality was having its say. As with humans, she had to work through her difficulties. I think her interactions with John (when he’s not pissed at her) and Eric (the library guy in “Self Made Man”) helped by actually reinforcing the positive inquiring aspects of the Allison personality. Ironically, the human who exhibited the most consistent disdain for the Tin-Miss probably did the one thing that helped most of all: she flipped an up-turned tortoise right-side-up and placed it out of harm’s way.
In fact, that single act might have been the catalytic event for the entire second season. The one that allows Cameron to recognize moral decisions and subsume her humane tendencies, and Catherine to see that humans aren’t all disappointing monsters.