I'm a fan of sneaking in small nudges to Earthdawn in the background of things; the players never need to know the whole picture anyway.
IIRC, that horror of all horrors captured dragons and put them in a sort of corrupting cocoon where they hibernated until needed. Maybe a construction/mining team in the aqualogy dug a little too deep, at the wrong place... Would semi-explain why a dragon would run amok like that.

Or the spirit thing - The aqualogy would prolly seem much like a caer to a newly awakened horror. Make it one that work through "social" means (as opposed to munching on everyone in sight) - Maybe bodysnatchers style so the PC's never know who's untainted or not.

Just came up with a more mundane idea, maybe it isn't one all-powerful entity: Have a cult infiltrating the whole structure over time, and now deciding to strike. A sizeable portion of the population and quite a few of the administrators have been reqruited. Maybe the cult plays it cool and rationally works towards making the whole installation a base of operations - or go all-out sodom and gomorrah, mass-sacrificing people in gruesome manners due to the leader's whims. It's all about which feel you want to convey, dystopian enslavement or horror and holocaust.
Oh, and throw in some kind of infathomable summoning at the end .

Wraith, Nomad, Will-o'-Wisp, Broken Bow, lots of unbindable spirits can shred any civilization, especially once you note the minimum force requirements on most of those and/or high speed advancement options. They also tend to make PCs either all go mage with their replacement characters or instantly run from anything that doesn't need a physical form to survive. A greater incubus at least can be killed with explosives and sharp things.

(from Critters, p. 24) "It is linked with sites of witchcraft trials and major sabbat festivals, and it tends to manifest at those places and times."

No worries.

I'm liking the merrow shaman idea, but there's no reason I can't do both. One of the reasons the PCs will be in this aquadome is to extract a marketing specialist who's been experimenting with incorporating magical elements into viral marketing strategies.

I'd already determined that the marketing guru from Aztechnology ('cause nobody spins better than the Azzies), and that he was Awakened. Leased by Saotome (the company in charge of the aquadome), the Azzie and his jaguar guards are working in a secluded part of the facility. No reason this spellweaver couldn't have been experimenting with a nomad.

With nomads running loose in the upper levels and the shedim/merrow shaman and its minions running loose in the flooded lower levels, it'd be a memorable scenario. Throw in some surviving civilians and the PCs' inability to distinguish between the "safe" survivors and those possessed by a nomad and you've get a hell of a cocktail.

Yes, but that falls back into the intelligence and tactics level. Any entity capable of surviving alone in a hostile environment should know how to quickly recognize real threats and respond accordingly. Even if the response is to retreat and try again elsewhere. Nothing can retreat as well as an unbindable spirit or fairy. Those two types can escape from pretty much any trap or opponent at whim, and return when and where they desire.

Runners aren't the only ones who will try to geek the mage first. However, some spirits may want to encounter the mage in a non-threatening way and then geek the mundanes. Afterward, the spirit and its puppet will collect the pay and begin more terrifying scenarios.