The idea that I'm running with for my own campaign is this: The Horrors haven't just been hitting Earth, but rather any world with a manasphere. Some of those other worlds have had folks already in residence. And in some places, the Horrors won big and became the folks in residence. Most of the time this just gave them a world in the physical plane as a new playground... until they won on a world with enough of a tech level to make arkship-type interstellar travel feasible. Of course, the Horrors need a strong mana environment to hang around (some of them can function just fine in lower mana if they've got a host), so the style of arkship that the PCs in my campaign will have showing up at their Earth is going to be basically a Neptune-size planet that's been hollowed out and filled with a biosphere. The Horrors-as-aliens are going to be a primarily biotech-based threat; conceptually a cross of the Bane from Tabula Rasa and the Yuzhon Vong from Star Wars. Short term (this campaign) will eventually be dealing with their arrival and the initial big brawl. Long term (future campaigns) will go beyond that once I've had a chance to really sit down and decide how things will or won't change for various folks in my SR setting.
I will note that this campaign wasn't originally put together for Shadowrun, but was rather brought into SR from d20 Modern when 4th edition came out because it was an easier-to-use system and the existing SR timeline was close enough to the one we'd put together that it didn't really need any tweaking at the level the PCs would be aware of. But it has been fun thinking about how all the various power groups of the SR world would react to this kind of outside incursion, especially when certain folks realized that the Horrors were the power behind it.
From a design standpoint, I haven't really needed to come up with anything overly radical or which deviates too far from what's already within SR (the PCs aren't exactly going to be the ones making frontal assaults on the worldship or taking them on in space dogfights, after all). Horrors, bug spirits, shedim, and the like are all represented at serious threats and will only become moreso once the new guys show up and start making friends. The shock troop and leader types of the new threat are unique to our campaign and are a serious enough threat by themselves to make a solid team of combat runners come through barely breathing.
So it is possible to introduce an alien threat to a SR campaign, just remember that you're working within a living setting with its own history, personality, and an internal logic that extends to the entire universe it exists in. Magic isn't just some strange way to view higher physics, it's something that permeates all states of existence in this setting. So I'd highly recommend making your alien threat not only aware of it but adept in its useage. Pick a couple of the things magic can't do in normal Shadowrun and think of a way for these guys to bend or even seemingly break this rule (my favorite for my new threat is that they can violate the 'no line of sight for spells through technology' rule by using what is basically a biotech-grown brain as the core of a kind of sensor drone that one of their initiates then mindlinks to... it gives them a distinctive advantage that can still be overcome by observant and creative players).
