This part of the walkthrough will take you through the final boss fights.
Temple Boss: Bellum
In a chamber with a pool of murky water, Link sees for himself the evil that is Bellum: a squidlike phantom creature with tentacles that have eyes on them. It spits out purple goo from its "mouth" that then forms into small goo creatures that have the ability to attack and harm Link. Plus, Bellum can use its tentacles to swat at Link wherever he's standing.
In the first part of the battle, as Bellum is in the pool of water, its body is covered with purple goo that we need to pull off bit by bit with the Grappling Hook so we can then pull its body toward us and strike its eye with the sword. Occasionally Bellum will drift away, so when it does this pull it back toward you with the Grappling Hook and keep striking him. After several hits, Bellum will lift itself one floor higher in the chamber, attaching its tentacles to the pillars and using one of its tentacles to strike at you. Avoid that tentacle and aim for each of the tentacle eyes with the arrows. Hit all of them and Bellum will fall back into the pool, where it will cover its body with goo again. Do the same thing you did before: pull all the goo off with the Grappling Hook and then pull it towards you so you can strike its eye repeatedly. It will then go back to raising itself one floor up, but this time will spit out goo monsters to slow you down. The tentacle eyes will also open and close, so you'll need to strategically hit the eyes when they are open. When all of its eyes are struck, Bellum will now go another floor higher, and in addition to its earlier methods of attack it will now occasionally detach itself from the poles and spin itself around a few times, trying to hit you with all of its tentacles. Try to keep yourself in a place where Bellum won't strike you with the tentacles, and keep aiming for the eyes when they are open.
When all its tentacles are hit a second time, Bellum will spit out a yellow glowing orb that Ciela will fly into. She will then suddenly be stirred as she experiences something strange. Oshus will now appear to tell Ciela that those were the memories that Bellum had drained from her. Ciela now remembers that she is the Spirit of Time and Courage, and with that memory comes the knowledge of a new power she can unleash to help Link defeat Bellum: the Phantom Sphere. When you get a Phantom Sphere, you tap on the hourglass icon on the screen, causing a frame to appear, and then you draw a figure eight in that frame to make time stop for several seconds. Everything in the room but Link remains frozen during that time.
So, now commences the next part of the battle. Go back down to the floor with the murky pool, and as you do, the staircases will now disappear. Then watch Bellum's movements: it will circle around the pool and then hover over it for a while before circling around it again. Time the use of the Phantom Sphere so that Bellum is in close proximity to you when you freeze time as it circles around, then strike its eye repeatedly with the sword. Keep doing this until Bellum returns to the pool, apparently weakened from the blows of the Phantom Sword, which means you have defeated him.
The Possessed Ghost Ship
After Bellum is defeated, the ceiling of the chamber collapses, with a column falling right on top of Link and Ciela. Oshus uses his magic to transport them from the chamber right onto Linebeck's ship -- and right on top of Linebeck himself! The sea captain brings Link over to the lifeless form of Tetra, which is now regaining color. Oshus has used some of his restored power as the Ocean King to bring Tetra back to life. Tetra is glad to be alive and is grateful for Link, Ciela, and Linebeck coming to her rescue. But this happy moment is soon ended by Bellum grabbing Tetra by one of its tentacles and bringing her over to the Ghost Ship, which it now possesses as organic eyes are sprouting up everywhere on it. It's now time to chase after the Ghost Ship and rescue Tetra again.
This part is a really tough naval battle, which you'll need a lot of hearts in your ship's health meter for. Otherwise, prepare to go through this again and again. As Linebeck takes the helm, direct the cannon to fire at the eyes on board the ship, meanwhile watching out for the purple bolts that it fires at you. Your ship will constantly move to one side of the Ghost Ship and then to the other, so keep the Ghost Ship in your sights as much as possible. Also the Ghost Ship will seemingly generate new eyes in places that you've already blasted. Don't worry too much about the regeneration; just keeping firing at the eyes until it is no longer able to generate them. When you've blasted the last eye, the Ghost Ship will go half-down into the water, crippled beyond repair.
Final Boss: Bellumbeck
As Linebeck and Link board the remains of the Ghost Ship, we will be asked to save our game at this point, which we might as well do. Suddenly Bellum causes the mast of the ship to fall right onto Linebeck's ship, sinking it along with Oshus who was still on board. The creature grabs Link and holds him captive along with Tetra, causing him to drop the Phantom Sword near Linebeck's feet. The distraught sea captain fearfully picks up the sword and uses it to defend himself against Bellum, who lets go of Link and concentrates its attention on Linebeck. Ciela helps Link regain consciousness long enough for him to see Bellum being held off by Linebeck, but soon Bellum wraps its tentacles around Linebeck and overpowers him. Linebeck throws the Phantom Sword over to Link before Bellum causes Phantom armor to appear on Linebeck, putting the sea captain under its control. So now we're fighting Bellum in its final form as Bellumbeck.
At the start of the battle, Bellumbeck will simply come toward you. Ciela generates a Phantom Sphere for you to attack him standing still, but the first time you use it will be worthless, as Bellum's eye isn't open. Ciela will now go behind Bellumbeck, and in the upper screen we can see the Phantom's back so we can be prepared to use the Phantom Sphere when the eye is open. But another problem comes along: Bellumbeck snags Ciela with one of his tentacles, preventing her from generating a Phantom Sphere. To break that control, attack Bellumbeck head-on with the sword until you lock swords with him, then quickly rub the stylus back and forth to give yourself an opening for a frontal swipe. Ciela is now able to generate a Phantom Sphere for us. Bellumbeck will now rise and use a broad swing of his sword. Avoid his swings and watch for Bellumbeck's eye to open in the back, then use the Phantom Sphere to freeze time so you can strike the eye repeatedly. When time resumes, Bellumbeck will be knocked back a good distance from us. After some successful strikes, the Phantom will use a tornado attack on Link after he gets his next Phantom Sphere. Avoid the attack and watch again for the opening of Bellumbeck's eye so you can freeze time and strike it repeatedly. Eventually Bellum will be so weakened that it will detach itself from Linebeck, resuming its original form before its body turns to sand.
Success!!! You've just beaten the final boss of the game.
As Bellum's body turns into sand, Link uses the Phantom Sword to capture it. Linebeck is now restored to normal, both apologetic and grateful, and Tetra is safe and sound. Suddenly, the Phantom Sword explodes and releases the captured sand into the sea. Then a great white whale emerges -- it is Oshus, having been returned to his true form as the Ocean King. He is grateful to Link for having restored him in full, and now has the power to grant Linebeck's wish. Ciela is surprised that of all the things Linebeck could wish for, the only thing he wanted was his ship back, but that was what Linebeck truly wanted now. The Ocean King tells Link that peace is now restored to the sea and that the Ghost Ship will not bother anyone ever again. Now is the time that Link, Tetra, and Linebeck return to their own world while the Ocean King and the three fairy spirits return to theirs. A white mist envelops the three adventurers as Link waves goodbye to his companion Ciela.
After the credits have rolled, Link and Tetra find themselves back on board the restored Ghost Ship, and Tetra's own ship pulls alongside it. Link and Tetra reboard their own ship, with Tetra wondering why the crew hasn't gone off to try finding her as Link did. The crew told her that she was gone for only 10 minutes, probably suggesting that her and Link's adventure was just a dream. As Tetra aggressively tries to convince the crew that it wasn't a dream after the Ghost Ship vanishes, Link pulls out his now-empty Phantom Hourglass as proof. But then he sees Linebeck's ship off in the distance, going to wherever Linebeck was heading. Link is happy to see that Linebeck's wish has come true.
And so the story ends.