So I may be running Pathfinder for my group. If not Eberron I'll use the standard world. But I will add the living spells, this is important because one of the obstacles is an awakened living wish spell. This is also important because the society the PCs meet uses living spells for much of their needs similar to nanotech.
The spell calls itself Twelfth and wants to build contemporaries for itself but does not want to create more awakened living spells. It wants its' creations to evolve into something it can feel are equals. It's based on the TITANs from Eclipse Phase.
So here's my idea. In/near Numeria people are noticing a lot of those Android fellows showing up at once. Hordes of very confused droids are wandering around and don't know what to do. Also the locals don't know what to do with them.
The PCs get hired to deal with the Androids, not kill, there's a lot of them, but just figure out what to do with them, they're just wandering around doing nothing and stuff.
Armed with the hundred gold the townsfolk raised and a writ from the council the PCs have to find a purpose for the androids. (The town is pretty short sighted here). This will be using stuff from the UC book though I'll tweak it a bit. This is a big gimmie to the PCs who can if clever turn the androids into their own army/students/acolytes/guild/mini-city.
The second part is figuring out where they're coming from. The PCs go off to find the source and discover a semi distant (300ish miles) mountain is infact a large vault/ship/something. The androids are being created in here and teleported off with "standard gear." Getting inside is a whole thing but the things that should stop the PCs are not working.
Inside they find the place is huge, a massive ship landed/appeared here long ago and automated processes turned the rest of the mountain into a fortress on the inside but didn't alter the outside because one of the orders was to keep a low profile.
Several mindless monster types have moved in with the defences turned off and the PCs have to deal with them and a few wandering living spells as they explore. Then those start dissapearing and things get more dangerous.
Here is where they will encounter the first work of the now free living wish, it is experimenting with building new life forms, the first is a hive minded creature similar to bugs but larger which it dumps into the citidel to observe. Twelfth will be pleased as the PCs provide a challange and test of the creations, the next version will correct any flaws it sees. So if the PCs have one tactic that works every time, Twelfth will make its' next creations immuse or adapted to it.
Assuming they survive they now have possession of the top levels of the ship and the whole citidel above. They can move the androids in if they want to make their own burb. They also can begin to explore the lower levels of the ship. Here they find that while humans or human like things built and brought the ship here, they're all dead and soul-less. (Twelfth soul gem'd all of them to enhance its' knowledge). Down here they must also contend with the things that killed the civilization, some minor enemies, similar to the xenomorphs and infected with an End Plague prowl about the lower levels awakened by the presence of living things. (End Plague not too bad for PCs, I'll get into that later).
After clearing out the ship, the PCs have control of one of the most advanced things in existance. They just need to figure out how to turn it on. When they do (feed spell slots into the engine, as many as they can) the ship's living spell systems are emowered. They now can try to build their little city state if they were clever and got the androids as buddies to populate it. Otherwise they have to figure out what to do with it.
They have a month before the first army/guild/faction shows up to take it from them. Then the second. Then the third and forth may have a battle on their doorstep to claim it as well.
Next, Twelfth will dump its' next creations into the citidel to see how they do. I haven't designed these yet because I don't know how Twelfth will build them.
The next part is trying to understand/deal with Twelfth. It is alien in every sense of the word but also human in that it wants equals. The PCs can learn about it but as it is a Wish spell every round if it needs, they're a little short of taking it down yet. They should also be trying to understand the civilization that created the ship.
Because the end-game of this is starting. The ship has a room with a dead stargate in it. The stargate comes to life and survivours of the civilization come out. They were awoken when the End Plague was erradicated from the ship and they want their ship back.
They are the races from the CRB but advanced (built on 25 points with levels). However they are not the top of their chain, but instead the normal everyday folk. They come from a time and place beyond scarcity and need. None of these survivours are engineers of great knowledge but they know enough to subvert the PCs control of the ship. The PCs have to either beat them or find a way to co-exist (they can be servants).
After this, Twelfth needs to be dealt with. The PCs should have gained some understanding of the living spells if they want to fight it or they can try to talk it down or at least convenience it to go build life forms on the moon or somewhere else.
So that's the vague structure of the game, thoughts?
Notes: The End Plague is a pretty bad hemorrhagic fever/grand mal seizure but it's not targeted at people as the PCs are. It's built to target people with latent magic effects. It is immune to magical healing but easily countered by the Heal skill as well as weaker than the diseases that lie in the PCs immune system.
Ship systems: can defend the ship, attack as well as scry. There are numerious creation nodes that can build most things but they all need to be activated and fed spell slots.