1 - Return to the Sealed Temple and open the Gate of Time.
Now that you've got the Master Sword, you can open the Gate of Time at the Sealed Temple. Meet the old woman there to make preparations, but before you can complete the ritual, a familiar rumbling rolls over the land...
2 - Defeat the Imprisoned to re-seal it a second time.
The Imprisoned has broken its bonds once again, and this time has taken on a more complete form. Groose has offered to help, so abuse him in the coming battle!
Dive back down to the fading seal at the pit of the Sealed Grounds and watch as the Imprisoned rises from its grave once again. This time it's got arms, but you have a new weapon of your own - a makeshift catapult constructed by Groose. Once he's prepared the catapult, you'll see his face appear as an icon on the D-pad and can call on him to fire bombs at the Imprisoned. This will stun the beast, giving you an opening to attack its feet, which otherwise send out shockwaves with each step.
The main advantage the arms give the Imprisoned is the ability to climb up to a higher level quickly. If this happens, either summon Groose to knock it down with a well-placed bomb or use an air vent to float up to the next level and slash at the boss's fingers to cripple it. Otherwise the strategy is more or less the same, although with the more frequent shockwaves abusing Groose is critical to avoiding damage.
Once you've knocked out the Imprisoned by cutting up its toes, it'll fall just like before, except this time you can't just run around it. Its arms block the entire path. You'll have to drop down to the level below, backtrack a bit, and use a nearby air vent to float back up in order to reach the sealing spike. Three complete jabs of the spike into its head and you can reseal it. The spell you need to draw is a bit more complicated this time, but works in just the same way.
3 - Approach Zelda so she can bless your Master Sword with the goddess's power.
With the Imprisoned out of your hair, return to the Gate of Time and proceed through it to meet with Zelda. She'll bless your blade with the Goddess's power, elevating it to its true form. Momentous plot twists abound that are best not spoiled here.
True Master Sword
Zelda has blessed your blade with the power of Hylia, completing it at last! Look at it shine with the power to slay demons! Now all you need is the Triforce and you'll be ready to smite Demise once and for all!
Just like you did with the Ballad of the Goddess, approach Gaepora and ask him what he knows about the Triforce. It honestly isn't much, but it's enough to give you a lead: seek Owlan and ask him about the great Sky Spirit Levias.
5 - Follow the clues to the Lumpy Pumpkin and deliver the soup to the Thunderhead.
Owlan knows enough to point you to the Thunderhead. You'll need a birdriding technique called the Spiral Charge to deal with Levias, but it's normally only available to senior birdriders. He'll make an exception for you, though, but only if you complete his training course. Strike through the targets with the Spiral Charge and the move is yours for keeps.
Once you've got the Spiral Charge, head for the Lumpy Pumpkin and ask the proprietor about how to lure Levias out of hiding. He'll give you his yearly offering of pumpkin soup with the instructions that you're to take it to the rainbow island in the Thunderhead. Scrapper can carry it for you.
6 - Defeat Bilocyte to purge Levias of his curse.
Once you've made the delivery, Levias will rise up from the clouds. He's infected by what looks like an evil parasite, which you'll have to purge in order to get his help. Use the Spiral Charge on the four eyeball stalks protruding from his sides, then dive onto his back to deal with the main parasite, Bilocyte.
Ocular Parasite Bilocyte
Bilocyte is the parasitic tentacle that has latched onto the sky god Levias and taken control of him. It fires noxious goo from its eye stalk, but you can repel the attack with your sword to launch it right back at the beast.
It'll spit hunks of poisonous goo your way, but you can repel them with the Master Sword. The direction you swing influences the direction the poison ball travels, so try to point it at his "sail" like appendages first, then aim them at his large eye. A direct hit will stun it, leaving you an opening to attack it with your sword at close range.
After a while the eye will start shifting positions, so adjust your reflexes accordingly to make sure you hit the attacks back in the right direction. A few rounds of hits and Bilocyte will fall, and you can ask Levias what to do about searching for the Triforce. He recommends uniting the songs of the three elemental dragons to form the Song of the Hero. Each region has its corresponding dragon: Fire in the Eldin region, Thunder in Lanayru, and of course the Water Dragon in Faron. You can pursue them in any order, so pick and choose as you wish. Chapter 18 of this guide corresponds to the Fire Dragon, Chapter 19 to the Thunder Dragon, and Chapter 20 to the Water Dragon.