Megara, I think her name was- even though AIs are technically sexless, she fell in love with Dodger, so I would presume that she was a female intelligence.
Deus is a corrupted abstraction of Megara, but while he was in the Arcology, he operated on thousands of Renracu employees, implanting cyberware apparently at random. A lot of this was headware memory, hard-coded to put some of Deus' programming while that employee was accessing the matrix (or asleep, and therefore unaware of the access). Some otaku became aware of this plot, and started eliminating these "nodes" but apparently they were unaware that part of the time, at least, Megara's code was more present, and she took control of the nodes active at those times.
That was the plotline before I stopped paying attention, and shortly after that, they wrote 4th edition.
Apparently Art Dankwalther's attempt to ruin Novatech and it's founder had not gone without blood being drawn- Novatech was in enough trouble that it's owner was forced to have a public offering to gather enough money to keep it afloat. This public outing, the largest in history, formed the company into NeoNet, now publicly traded. Villiers tracked down Dankwalther and dropped a bomb on him, as far as I know, but the Novatech public offering went through other significant problems. With so many nodes online, Deus seized control of the network, coming online in the matrix fully for the first time since his desrtuction in the Arcology, and declared himself the God of the matrix. The Grid Overwatch Division fought him, and were losing, when someone dropped a train on him- almost literally. The Organization Winternight actually used an EMP Nuke on the area, crashing not only Deus' network of nodes, but the matrix as a whole.
Since the matrix was down anyway, the megacorps decided to push a new technology, a wireless matrix, rather than working to repair the old matrix. This matrix, version 2.0 if you're using old 1980s teminology, functions completely wirelessly, and has come to dominate life in a way that the old matrix never did. Oh, also Otaku no longer suffer from fading. I'm not really sure why. But they're all technomancers now. And there are no more riggers. And deckers, instead of being known by the name that they've been using for 60 years, are now called hackers, like they were back in the 1990s.
(I have major problems with the points in the last paragraph- most of my problems with 4th edition's storyline, actually)
Okay. Does that answer any other questions?
-kv