After completing the prologue of Pillars of Eternity 2 Deadfire you will arrive at Port Maje Island not in the usual manner - as your ship had been destroyed. Thus, your main objective will be finding a way to repair your vessel. This is connected with the quest Stranded, that you will receive automatically after the shipwreck. Simultaneously you will get another quest, To Hunt a God. These quests coincide with each other to a large extent.
To complete the Stranded quest, first head to Port Maje Harbor. There, you will witness a conversation between governor Claria and Ikawha. Later the governor invites you to Governor Clario's Estate, in return for a favor the governor offers to repair your ship.
Your objective is the Engwithan Digsite - there you will encounter a group of people (along with Aloth, who can become an addition to your party), but most importantly you have to dwell into the Arena sub-level, which is the main dungeon in the digsite area. There, you will find Oderisi's corpse along with his notes. In addition, an interactive scene connected with the quest To Hunt a God will occur.
Now, you can leave the dungeon and head to Port Maje Harbor, and in particular to the Governor Clario's Estate. After a brief conversation the governor will agree to repair your ship. Return to the starting location, that is, to Vilario's Rest. A short scene will occur, your ship will be repaired and sent to sea once more.
The ship needs a proper crew; the minimum is five sailors, that you can hire at Port Maje Harbor (visit the harbor or the inn, The Kraken's Eye). Remember about stocking up in basic provisions and purchase some healing items, repair materials, and cannon balls.
You can find more information about the Stranded quest in our official walkthrough; and as for the ship travel, you can check "Traveling by ship" section.