So the initial abduction's goal was to kidnap her and copy her consciousness, which apparently succeeded. Their ultimate goal I'm guessing is robot freedom or something like that.
One thing is realistic about this series' technology, and that is the idea that a successful AI is a black box. A successful AI, developed via continuous evolution from a basic state, will likely look like an absolute unmanageable mess from a raw code perspective, and two separate AIs could be so different as to be indistinguishable.