As far as I can tell, the full extent of information available on the end of Saito Californian Protectorate is this:
QUOTE
Shadowrun 4th edition, page 34
CalFree finally saw the last of Saito, but not the last of its woes. In early 2069, a pair of major earthquakes coming from the San Andreas Fault line and the San Pedro Shelf caused widespread flooding and destruction, killing tens of thousands.
Shadowrun 4th edition, page 42
In any case, [Mitsuhama Computer Technologies has] established quite a presence in CalFree over the last few years, taking a lead role in the control of San Francisco following the fall of rogue General Saito.
Sixth World Almanac, page 176-177
In late 2068, California, together with corporate backing (primarily from Ares), retook the Bay Area from the rogue General Saito. [...]
> Since many of you were busy elsewhere, I’ll just give you the cliff’s quicky version of the end of Saito. It was beautiful. While a bunch of local groups ran piecemeal against Saito — from pirates to the dwarfs of Halferville to the occasional runner team — the turning point came when Ares stepped in. They made noises that it was concern for their Silicon Valley area, but I think Damien finally just got pissed off (or maybe bribed? blackmailed? who knows, who cares). With Ares special forces running the op, dozens of groups joined up. We’d lacked a cohesive vision, and we finally had one. I saw Ares special forces working side-by-side with runners and pirates, Mothers of Metahumans (MOM) ladies sheltering troops in their basements and feeding us PB&J, Ancients gangers running weapons, even a contingent of shamans from Shasta. It was huge, well-organized, and we completely smashed them. Everyone was flying high for days from all the good feelings... or maybe that was just those brownies those hippy ork ladies kept handing out...
> Sounder