One thing that I did read about was that Gov. Shultz was attending a meeting inside the Arc when it went offline and as events spiralled out of control Lindstrom was voted in as the acting Governor. However, I didn't seem to find any mention of what actually happened to her and I can't see Deus letting such a valuable puppet get away.

Are there any canon references in any other sourcebooks, other that 'RA:S' or 'Brainscain'? Or has it been deliberately left open so the GM can develop the storyline?

i emailed jason levine about this some time ago. he said that there wasn't anything being done with it that he knew of. given that there have been several books that've come out since BS that haven't mentioned her, i think it can be safely assumed that she disappeared permanent-like during the shutdown.

What mfb said. There's no mention of her other than the "missing" bit in either RA:S or Brainscan.

Short story: Deus (mad Renraku AI) took control of it.

Spoilers are easy, just make a '[' then type 'spoiler' then add a ']'. At the end, do the same except '/spoiler' between the' [' and ']'

So about like this? Oh and you can keep laughing cause I really did click on all the differnt spoilers... bastard.

He downloaded his code into people's headware. These people are now out of the Arc and re-compiling Dues on the 'Trix.

3:00 P.M.
Like hundreds of other people, Liz, Josh, Doug, and Tony meet in the Matrix. Their minds come together easily, swiftly, as if guided by a single will. They join. They are one. More minds enter the pattern. They grow. They remember.
And somewhere in the Matrix, something free begins to take shape.

Deus was the second AI to spring up in the Renraku AEP. (That's Arcology Expert System to the uninitiated) The first was Morgan (later Megeara after one of the Furies of Greek legend) and it was her eventual re-capture (and the subsequent incorporation of her code into the AEP) after she escaped to the Matrix that gave birth to Deus. Renraku Computer Systems (hence ACS) fearing that if another AI were to develop that it would flee tied the AEP program to its physical mainframe. At the behest of it’s CEO Inazo Aneki it also had a killswitch installed to guarantee control if an AI should arise. It was this act that served as the “x” factor that allowed Deus to gain self awareness. RCS had no idea that there was a nascent AI in its Arco-block until Deus came out of the shadows and shut the whole damn thing down. With a following compromised originally of fanatic otaku that "he" had brainwashed into thinking "he" was the Deep Resonance (the quasi-mystical “spirit” of the Matrix that is responsible for the creation of all otaku) he began creating an army of cybered slaves. In addition he had already built a formidable force of some of the most advanced drones on the planet. Once he had closed the place down and set up shop he began conducting experiments on the 100,000 plus captive residents of the Arcology. The purpose of all this had remained a mystery until Brainscan when it was revealed that the whole thing was a way for Deus to try to get around his programming tying him to the mainframe. End of story for now.

In Threats 2 there is a chapter named The Network. It deals with the people (at least thousand) that have both the code of Deus and Megeara in their heads. The people with the code are refered to as Nodes and a node can either be por Deus or pro Megeara. All nodes are trying to recreate an AI, but depending on which factor is in majority (not everyone is connected to the Matrix at the same time) the recontruction takes different paths. I haven't seen anything newer than this.

note that members of the Network all have otaku abilities (Deus has discovered a way to grant these to adults), and are all subtly but heavily modded. they should be pretty badass--good combat skills, good stats; a good starting point might be the stats for Blues from RA:S.