Initially, you’ll have go to from pillar to pillar here via the Clawshots, in a similar manner to how you reached the Goddess Cube from earlier across the large pit. At the end, drop down to the ground to find a crumbling bridge. Clawshot over to the opposite side to a large, but mostly-enclosed area. Be wary - wandering around can find you a lot of Yellow Chuchus and Arachas, but you can also find Lanayru Ants if you’re into that sort of thing. Also be sure to use the Bird Statue nearby.
Anyhow, to the north are a bunch of crates. Manually climb onto them, then Clawshot over to the northwestern bunch. On the other side, drop down and go into the alcove. Defeat the bunch of Aracha that fall (and likely Jelly Blobs; I got like four or so here). Afterwards, activate the nearby Goddess Cube with a Skyward Strike. Exit the alcove and go back over the crates.
Afterwards, go west and onto the pier. At the end, you’ll find an old robot and a boat. Hit the Timeshift Stone on the boat to transform the desert nearby to water, activate the robot, and make this Timeshift Stone permanently active (you’ll see why). Speak with the robot for a bit. You’ll learn that he “recently” lost his crew and ship, so agree to help. You’ll first have to get his sea chart (ahhh… Reminds me of Wind Waker), which is marked on your now-extended map.
So, first, you’ll learn how to control the boat. The Control Stick controls which direction you move (it’s weird, operating without an accelerate). The A button controls your boost, which has a Stamina Meter. The B button activates the cannon, with its aim operated with the Wii Remote’s point and shots with the A button. Anyhow, your destination is the Skipper’s Retreat, which is south-southwest/southwest of the pier from earlier. Once you arrive there, disembark the boat.