Before you continue to the final part of the game, you need to reassemble the Triforce. You also you might want to have the following things:
I recommend putting three fairies in bottles and granny's soup in the last one.
Tower of the Gods
All that's left now is to warp to the Tower of the Gods and sail through the arch for the automatic scene.
Mysterious Underwater Place
Get out of your boat and go into the castle. Notice how the hero statue is smashed up and things look generally out of sorts. Equip your Picto Box. Go down those stairs that led you to the Master Sword way back when, and walk up to where you got the sword. Watch the scene.
The enemies that you face next are Mighty Darknuts. This is one of only two opportunities that you will get to take a picture of one. Kill one of them, then walk near the edge so that the other one follows you and gets close to the edge, then run to the other side of the platform, turn around, and take the picture.
To kill the Mighty Darknuts, you can cut off their capes with your sword or burn them with a fire arrow, then use parry attacks as usual. Then go upstairs and watch the scene.
I recommend making the figurine of the Mighty Darknut now so that you can have three free spaces in your picto box for the upcoming part of the game. Just return to your boat and warp to the Forest Haven to do so, then return to the Tower of the Gods to go back underwater.
Go through the far door now. Keep walking and eventually you see a sort of purple barrier in your way. If you don't see it, you will bounce off of it. Cut it with your sword.
From there, just follow the straightforward path. After the monsters, you reach a place that you have to hookshot across to. In the middle platform are some keese. Just kill them with the hookshot or boomerang. Then use the hookshot to get into the cave. Go through the door at the end to enter Ganon's Tower.