In Shadowrun the PCs are as apt to be working for the bid bad as stopping them ;-) (at least up until late into the process)
In one of the recent books it was stated that the current version of the wireless matrix was created a bit by accident, when evil experimenters made a network out of 100 technomancers. It had useful features so they fed more computer power to it and grew it out to the grid we love to loathe now. They eventually realized that those foundational technomancers had died, but the matrix carried on all the same. Perhaps your big bad could be trying to take it down because they know this, and are somehow trying to avenge the technomancers? (or alternatively feel that it is inately corrupt because it was created by technomancers). (I think it helps when the bad guy is not just trying to destroy things, but has a cause, no matter how crazy it is.)