The final battle.
From Nabooru Link is able to learn a little about the Gerudo and discovers that they are a race in which woman are only born, with the exception of one male who is born every one-hundred years. That male then has the right to be leader of the Gerudo, but in the case of Ganondorf he was not satisfied with merely ruling over the Gerudo and sought to rule over all of Hyrule as well. Then to discover that Sheik was in fact Princess Zelda was a shock to everyone––including Ganondorf himself. Even Link, who had perhaps been the closest to her, didn't realize who Sheik really was. Feeling saddened over having been separated from Zelda again, after only being recently reunited with her, Link is determined to rescue her and defeat Ganondorf. As Link gets up to leave Nabooru decides to accompany Link in order to teach a lesson to Ganondorf that there are some things that even a thief shouldn't steal.
Link and Nabooru arrive at Ganondorf's Castle. Shortly after they are ambushed by some of Ganondorf's minions, but they are no match for the two of them and are easily defeated. Wondering how they are going to reach the floating castle Rauru's voice is then heard. Telling them that the seal is released Nabooru is able to awaken as the Sage of Spirit. Disappointed that she will be unable to fight by Link's side she promises to continue supporting him in any way she can. With the final sage awakened the six of them use their power to create a bridge in which Link is able enter the castle to defeat Ganondorf and rescue Princess Zelda.
Fighting his way through the seemingly endless halls of the castle and waves of Ganondorf's minions Link eventually finds Ganondorf. Entering a large room Link finds him playing on a massive organ and Princess Zelda trapped in her crystal prison floating right above. Link then notices something glowing on his left hand which appears to be the Triforce but with one of the triangles glowing more radiantly than the rest. Ganondorf then speaks, saying that the Triforce wants to be whole once more. When he obtained the Triforce there were two pieces that he was unable to obtain––the Triforce of Wisdom and the Triforce of Courage––and now that all three had been brought together he sought to take them and become the absolute ruler of the world. Unwilling to let it happen Link voes to protect the Triforce and defeat Ganondorf.
Casting a dark wave of energy Navi is overwhelmed and unable to help Link, forcing him to fight on his own against Ganondorf. The final battle between good and evil then begins. Dodging each of Ganondorf's strikes Link works to close the gap between them, but is nearly hit by a more powerfully attack. They continue to exchange blows until it looks like Link may be defeated. As Ganondorf prepares a powerful spell Link decides to throw all he has into one last attack and throws it back at him. Link then catches him off guard and in one swift strike Ganondorf collapses to the floor, defeated. With his defeat Princess Zelda is freed, and is once again reunited with Link. This moment is short lasting, however, as the castle begins to collapse. Realizing they don't have much time they quickly escape from the castle before it collapses on top of them.
Once the dust settles Link and Princess Zelda look over the remains of Ganondorf's castle, relieved that the fighting is finally over. A crashing noise is then heard. Curious, Link approaches the wreckage and investigates the sound. A figure then emerges which turns out to be Ganondorf. He's still alive! Filled with anger and hatred toward Link Ganondorf uses the Triforce of Power and transforms into a monster known as Ganon. Ready for another round the two engage in combat once again. This time, the odds seemingly against Link as his attacks appeared to be ineffective against him. Link is then struck by Ganon, causing the Master Sword to be thrown from his hand and knocking him out. Landing behind Princess Zelda she knows Link needs it in order to defeat Ganon, and picks it up, throwing it back to Link. Ganon's attention then shifts to Zelda, but he fails to notice Link wake up.
Link: Ganondorf... You're still making the same mistake. Don't count me out...till the fighting is done!!
‐ Volume 2; Hero of Time - Chapter 9
With Ganon's back turned toward him Link strikes at his tail, nearly cutting it off. It is then discovered that the tail is his weak point. From there the fiercest battle yet takes place with each side exchanging blows until one move leaves Ganon open for one final strike. Falling to the ground the Master Sword begins to glow, indicating that the sword is at its full power. Delivering the final blow to Ganon Zelda orders the six sages to open the eternal gates and banish the evil king into the distant netherworld. The battle is finally over.
The storm clouds part and peace returns to Hyrule. Thanking Link, Princess Zelda tells him that Ganondorf is now sealed in a place of eternal darkness. She also tells him that with peace returning to Hyrule they must part ways, and apologizes for drawing Link into the conflict. As her duty as the seventh sage she claims she must put the Master Sword to sleep and close the Door of Time. In doing so the pathways of time will become impassable. She then asks that Link give her the Ocarina of Time so that she may send him back to his original time. Although this shocks Link he claims to have not been drawn into conflict and that he instead fought for her. Silence then descends upon the two of them as he gives Princess Zelda the Ocarina of Time. She plays a song and thanks Link once again.
When the light fades Link finds himself back at the Temple of Time as a child. He then smiles at the Master Sword, which now sits in the pedestal, before he turns to leave. With the journey over Link sets off to begin another, but not before one last visit to Princess Zelda.