Making the harbour an INSTANCE for a quest is a great idea..
Talk to the questgiver and you port into a "version" of the harbour where an invasion has taken place..
(an extension to the "invaders" quest maybe?)
all your favourite npc's are fighting or dead or fled..
When you've finished the quest, an npc cleric walks around casting true ressurection on your favourite npc's and life goes back to normal. Maybe freeing this cleric is part of the quest.
Having house deneith the "fortress" attacked would also make a good "time zone" instance