Plot Your Own Course by Ship
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Pillars of Eternity II: Deadfire is a sequel where you pursue a rogue god over land and sea, and the sea half of that is handled by a ship you captain yourself.
The ship is a stronghold
The store is explicit that the ship is more than a vessel for exploring: it is described as your stronghold on the seas. Treating it as a base rather than transport changes what you spend resources on, because it is the thing that carries you between ports and back again.
Upgrade the ship, choose the skills
You upgrade your ship and crew, and you choose what skills you improve in order to survive dangerous encounters along the way. Because that choice sits with you, the ship doubles as a progression system: what you invest in decides which encounters you can walk into.
Plot your own course
The Deadfire is described as a vast unexplored archipelago region, and the store invites you to plot your own course by ship, discover new places, interact with the inhabitants and take on a variety of quests at every port. That is a course you set rather than a route you are given.
Who sails with you is covered in building a party of seven companions. How the fights resolve is covered in trying the turn-based mode.