@Thomas,
Thomas wrote:
You make two very good points rosborne.
Yes, I did confuse the planting of the virus with the infection of the traffic grid.
And yes, you are right she would have known about the explosives if it was her factory.
Actually, I'm not certain about my own theory yet. A lot of things don't quite add up, unless I missed small clues in the story so far.
If I remember correctly, something John Henry said caused Catherine to go running off and destroy that warehouse, but it's not clear to me how she found it so quickly unless she simply extrapolated from the clues that John Henry revealed to her.
My pet theory at present is that both Skynet and [future] John Connor have sent back teams not only to kill/protect [young] John Connor, but also to alter Skynet's future directly.
I think Catherine is part of future Skynet's plan to facilitate Skynet itself. And I think the "other" machines (including worms in the system) are part of John Connor's attempts to alter Skynet's future.
The T-1000 which came out of the box on the Submarine said that the answer to John's question ("will you join us"?) was, "no". This implies that the future John Connor believes that some aspect of the future Skynet algorithm can incorporate symbiosis (or at least partnership). This may be something he is trying to implant into their system by altering the code which will eventually become Skynet. (on the other hand, I could be completely wrong).