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Long story short: I snatched Bates' journal from his chest, and after reading it, I sold it to Appleby, who later passed on the excruciating past of Bates to the press. Meanwhile, I went and explored the Black Mountain mines, and now I'm supposed to go to the Isle of Despair. Problem is, after I went back to Tarant (unbeknowst that the people know I was behind revealing Bates' true story), I found out that Bates has skipped town and I now have no-one to talk to about the next step in the main questline.

So, who's the person who could actually give me some useful information? Or can I find Bates somewhere else and let him tell me what he knows?
This question / problem has been solved by krakadylaimage
You don't need Bates, although you'll miss out on lore - but not on main story. You got your next destination already - Isle of Despair, so all you need is a captain willing to sail you there. Ask around the docks. Oh, and mind you, Tarant's not the only place with docks.
That's good advice, thank you. I guess the lore-thing was what I was most worried about. That and role-playing; I wouldn't want to advance to a certain city just because _I_ know that's where I need to go, although my character doesn't (you know, metagaming). Anyway, asking around the captains makes sense.