It's just kind of a squabble between various factions, and ultimately you have to squash them like little bugs in comically easy fights and then do whatever you want. I guess that's kind of a problem with the whole game, though - there's no real antagonist. No final boss, no attempt by the gods who don't agree with you to try and stop you, it just. I found myself almost in shock that the game just. You don't have to convince him or your party members, they just go "yup whatever you want" and then they do it. The game makes you kill the Queen to even leave, then you get to the island and it makes you kill the head Vailian guy (who was a dick anyway, so whatever), then you go talk to Eothas and have what was only slightly better than the rightfully-maligned "press button to select ending" choices of Mass Effect 3 and Deus Ex: Human Revolution. I didn't feel especially comfortable with them (and the way the game goes "hey go assassinate the queen for us" and if you decline, they go "WE CANNOT ALLOW YOU TO LIVE" and immediately turn hostile was just awful), but they were. And they do! It's a decent reason for them being there, and they're relatively decent people.
The Rauataians are unambiguously colonizing the entire Deadfire, and assuredly forcing their customs/traditions on the native people, but they're also going to Ukaizo to try and figure out if they can stop all the storms that make their homeland borderline uninhabitable. The Vailians just want to mine some shit probably, and the pirates are pirates.
The Huana just want it because of some sort of weird "this is our ancestral homeland" thing that turns out to be, at best, partially true - it's the homeland of most of the kith races or their ancestors.
I'd argue the least-bad one is probably Rauatai/Royal Deadfire, in that you DO have to assassinate the queen/overthrow the Huana, but they're also (for me) the group with arguably the best reason for actually wanting to go to Ukaizo. I'm fairly certain there are no "good" endings, at least it seems that way.