I don't think its that implausible. I mean, some of the Civilization games actually allowed you to build underwater cities. (Mind, it was so far in the future that unless you desperately needed to escape an irreprably irradiated surface it was just a pointless diversion).
Mechanically, it all depends on IF the Titans thought to designate underwater (and for that matter, underground) areas as city sites. If they did, then you'd need a side with Water Capable units or allies so you could actually inhabit the city in any meaningful sense. While normally I couldn't see a side like FAQ or Jetstone being able to take advantage of this mechanic... maybe, if the tendency of coastal cities to pop Seafarer units carries over to other specials. Like underwater cities popping Water capable warlords (or for that matter underground cities popping warlords with the Digging special
) it might be doable. You could transition into a side that's an underwater power.
If none of that applied, I imagine that a hypothetical race of Mermaid/Merman Natural Allies (which there has got
to be, it's just too iconic) could make little non-city villages or "camps" underwater. Hmm. I suppose a Dirtamancer with a SCUBA like magic item could probably build some kind of fortification or dwelling down there.