Through the locked door near the start of the dungeon, Link comes across the miniboss, the pirate captain Scervo. Scervo’s got two swords, but one hand is a hook, so he can only use one at a time. The fight is on a long, narrow walkway, and Link and Scervo try to knock each other back – Scervo trying to Link drive into a spiked wall behind him, Link trying to make Scervo walk the plank. The first two times he’s knocked back, Scervo recovers but loses his sword (and the second time, his sword arm) and brings the spiked wall closer to Link. The third time, he loses the hook hand and falls to his doom, leaving behind a treasure chest. Fi pops up to express admiration for the fact that he’s managed to survive all this time. The treasure chest has the final item, the bow; Fi… oh, Lord. “Your bow’s elasticity can propel arrows through the air with great force, allowing you to strike your targets from afar.” If I could believe this was meant to be parody, it would be hilarious. Fi also describes the bow controls [1], and for those unfamiliar with the mechanic from earlier Zelda games, notes the bow can activate eye switches, like the one on the deck.
Shooting the eye switch causes a Timeshift Stone to rise in a cage atop the mast, which brings the ship back to life. Unfortunately, that also means all the Bokoblins come back, so there’s a sequence of clearing the deck of Bokoblins. After it’s done, Skipper comes aboard to thank Link for his hard work and ask him to rescue his crew from the brig. Before starting that, there’s a heart piece to be claimed by Clawshotting down behind the ship.
As Link explores the ship, Fi calls attention to the ventilation shaft in the ceiling, allowing Link to shoot the Timeshift Stone on the mast. It might have been nice to have a chance to figure that out myself, but I can see it being a helpful hint if someone gets stuck. (On the other hand, that’s what the Sheikah Stone is supposed to be for….) It’s kind of disappointing only having one Timeshift Stone for the whole dungeon after the mobile timeshift fun on the Sand Sea and in the Pirate Hideout. The brig is blocked off by an electrical gate, so Link needs to sneak in through the engine room to get the crew out. To do that, he first needs to activate two power generators to make the engine room work. Once it’s done, Link goes through the smashers in the engine room and lets the crew out the back door; they give him a key to the captain’s cabin, where he finds the Boss Key.
With the Boss Key, Link can finally enter the control room; as soon as he does, a bunch of tentacles start popping up through the ship. As Link heads to the deck to see what’s going on, Fi pipes in: “The current situation is difficult to determine with complete accuracy, but signs indicate that this ship is under attack.” Fi has been at her worst throughout the dungeon, but… wow. She does give the useful hint that Skyward Strikes are necessary to sever the tentacles and escape, but again, maybe give the player a chance to figure it out on their own? (“Master, your weapons appear to be ineffective. However, sacred power may be able to cut through.”) Then, Link gets to the deck, where he finally sees the abyssal leviathan face-to-face, and…

I’d say this would be more at home in Wind Waker’s art style, but that game had Big Octos that actually looked like terrifying sea monsters.
In the first phase of the Tentalus fight, tentacles pop up through the deck and Link cuts them down. After four tentacles are gone, Tentalus shows up and tries to smash at Link, while Link tries to shoot its eye. This causes it to fall onto the deck where Link can hit the eye with his sword. This repeats three times, then Tentalus smashes the deck and Link has to scramble to higher ground. Tentalus reappears at the other side of the deck and attacks Link with its hair tentacles. These can be cut with normal sword strikes, and after a while Tentalus stops, leaving its eye open to attack once again. After a couple rounds here, Tentalus is defeated.
With the monsters gone, an altar pops up, Link Skyward Strikes the crest, and Nayru’s Flame ignites. Fi absorbs the flames into herself, and with no walls to bounce off, goes flying off into the sky. Unfortunately, she comes back, although this does allow her to shoot the flames into the sword. The ability gained here is incredibly useless: four extra dowsing slots, which by talking to the right people, can be calibrated to search for Goddess Cubes, Gratitude Crystals, treasure, and rupees, in addition to the three base slots for a primary quest item, a sidequest item, and hearts. Woooo. The lower left piece of the Triforce shines on Link’s hand. Back at the port, Skipper says he and his crew got the ship back together after Tentalus’ attacks, and wishes Link well in his quest.
Next: From an awesome robot buddy to… him. Oh, joy.
[1] Thankfully, pulling back the Nunchuk to fire arrows is optional. On the other hand, motion control to aim isn’t.