Fridge Logic: Among other things, why on earth wouldn't a sapient supercomputer with the ability to invent new technologies not make virus protection one of its first priorities? The events in the movie indicated that Will could have even made up his very own programming language if he wanted to, heck he could have probably built his own private internet.
One of several Plot Holes in the movie. The filmmakers pushed the whole Science Is Bad and Scale of Scientific Sins. Yes, it is a bit of a stretch to believe that Will only wanted to help (what with A.I. Is a Crapshoot being such a prevalent trope), but to "kill" Will with a virus, and accidentally nuke the entire Internet with him was just taking it too far.
Well, he was uploaded into that system, that language. He may not have been able to change or alter it too much...I mean, can you cut open your head and pull out fistfulls of brain and then just reconfigure it at will? Pun intended. It's likely, based on what is shown in the film, that he was now integrally part of the world computer network, wholesale, and it served as his "brain", as such altering the language and the way that it worked would be the equivalent of preforming neurosurgery on yourself, while conscious, without injury. In other words, impossible.
While a worldwide blackout (or every computer system in the world being taken over by an artificial superintelligence) is certainly very dramatic, in reality a great deal many computer systems (including those which are probably the most important ones, precisely in order to prevent such an intrusion) are physically isolated from the internet and no amount of intelligence could've let Will in them (unless he's gotten his nanomachines to do it near the ending, but this messes up with the film's continuity).
The movie does say that there are pockets of technology still working. The virus almost certainly wrecked worldwide and mass communication, so even if something is still up and running it'd be hard to advertise that fact outside of a certain radius.
My takeaway was that the nanotechnology had permeated the world's networked systems, including those bits and pieces, and therefore it tore it apart when Will was shut down. Or put another way, he saw the nanotechnology he created, and used it, like his body with the central control unit (the underground thing) being closer to a heart than a brain—-which would be the network—so even if all of your organs still are perfectly functional when your heart dies, they become effectively worthless without something to pump blood to them and die within hours at best if the heart is torn out. So when the nanotech shut down, it basically meant the network died from "blood loss".
Why was the garden the only place their intelligence survived? If all that's required is a poorly built backyard faraday cage, then there should be dozens, if not hundreds or thousands or TENS of thousands of pockets of nanomachines spread across the world. Every wire warehouse should have hundreds of tiny pockets in them alone. If a small faraday cage really could protect them from the virus, then the virus should have been completely ineffective.
