I don't have the book until my pre-order from B&N comes in, but I've been speculating since the SRD was released.
Right now, the primary idea is a psionics-based campaign, involving alien DNA (or whatever they use), or hybridization or something close to that.
Here follow the most basic ramblings I have so far. Input is welcome.
The basic idea: The Civilization on Alpha Centauri II was dying. They had bred too much and used up the resources needed to maintain a technological civilization. With no asteroid belt or moon nearby to mine, they were eeking out an existance with robotic probes (they were too fragile to withstand the g-forces needed to escape the gravity of their homeworld -- or some other rationale that they themselves cannot go into space) stripmining the gas giant moons. Even then, Civilization would end in less than a century.
This was 200 years ago.
Unable to go into space themselves, they fired robotic probes towards the nearest stars. They knew that Earth had carbon-based life on it, as well as planets circling Tau Ceti and Epison Indi. The probes contained near miraculous nanotech devices, and copies of their (DNA). If they could not travel in space, they would rebuild another race in their image...
The probe for Earth was struck by asteroidal debris, something the designers didn't plan for. Most of the probe was destroyed, but some parts survived to rain down across Earth over the years. The largest part, the heavily armored central computer core, plowed into the Russian countryside in 1908 and was one of the first parts to hit. The propulsion section following it down blew up (this is the huge flash and bang people saw) and drove the computer core into the ground. (Hmm. Why hasn't it been found yet? Maybe very small? Diffused into the soil somehow? Maybe it's in the Kremlin basement?)
Later sections landed in Roswell and other places, alerting the authorities (or those behind the authorities) that We Were Not Alone.
The nanites were damaged as well. The section with that stuff in it hit the ocean in 1923 and promptly diffused into the biosphere. The damaged nantites, when they interact with terrestrial carbon-based life forms, produce (organs? 'tumors'?) that allow for manipulation of quantum phenomenon and energy states: Psionics.
Whales, dolphins and related species are vaguely psionic and self-aware because of this.
Because of the damaged nature of the nanites, not even a small percentage of them really work correctly. Most introduce this change, then die off. People gain psi powers.
Some keep working, though, to change creatures.
Possible 'ultimate form' produced by a correctly-working nanite group: Illithid! (Aboleth? Fits the alienesque desc, certainly, but it's hard to have one of them masquerade as a person. Unless heavy illusion powers were involved, per They Live?)
The self-aware computer core buried under the Russian soil still attempts to control the nanite batches. People get weird disconnected dreams because of this.
Power Groups
US Military. Real X-Files territory here. They know things.
Russian Military, or intel. They suspect things. Currently they have the highest understanding of psi phenomenon.
The Computer Core. It communes with the 'ultimate form' aliens? Or they are trying to control it?
The aliens. The changed ones. They are powerful psis, and have an overwhelming drive to breed and control.
More ideas needed, of course.
