Arguably one of the hardest tasks to figure out is getting the Setzer. To get it you need to go to the cave at the other end of the map and defeat a series of guardians and activate the ship. While I don't think it is required to do, you might need to be in chapter 7, liberate Bazz (it's the fourth expert mission), get a quest and then complete it by going there, but you should be fine just going there.

Once you defeat the four guardians and activate the ship, you can enter the final room where you'll find a crystal and can pilot it. Doing this will unlock the trophy/achievement and send you in the air to fight dragons/other ships. Make sure to destroy 50 of those, since that is related to another task.