When can you start capturing other ships? is it part of the story or do they just appear on the naval mission map? I have done one mission that was labeled as a privateer mission but it was just the same as all the other ones (find enemy ships, sink enemy ships)

You don't capture ships in the game. You board ships a couple of times but that's very scripted.

Is it part of the main story though?

@Mister_V: There is one ship boarding that I've encountered thus far in the main plotline, and I'm guessing that any others are in the optional missions.

There is the chain shot ammunition that you can choose to use at any time but I've not been successfull in boarding a ship outside of the scripted instances.

ah, thanks for the info guys.

I don't think I ever will. Just threw my controller across the room due to a shitty chase sequence where connor refused to stay on course and decided that jumping into bushes and running up walls was a better idea than following the person.

that mission Is terrible. And that for the bonus it wants you to do it without barging into anyone is laughable.

That chase we speak of now is the worst of them all. I literally ripped my shirt because i was furious on where the hell to go to chase the guy. And of course there's a thick crowd of people to not bump into at all. To stay on topic though, the only way to board ships is with chain shot from what an above poster said. I haven't started naval missions to truly know more about it. I'm currently trying to liberate cities and get my assassin recruits together. Harder that the last games by the way.

Have you tried using your seamen?