Here's an idea for a basic plot. The game opens with a re-telling of the events of Skyward Sword. The game opens with Link and Zelda living near the resting place of the Triforce. Link suddenly has a terrifying nightmare that something terrible is going to happen. He grabs his sword and runs to the shrine where the Triforce is kept. There he sees the main villain: (Ganondorf of Ghirahim I would think) and some monsters kidnapping Zelda. Then the main villain reaches out and makes a wish on the Triforce. He wishes that the Surface be changed into a land of darkness and evil. Then the entire world becomes a terrible Evil Realm. A twisted and dead land. Link goes to the Master Sword pedestal, but finds it has disappeared. Monsters are everywhere and Link is unsure what to do. He then sees a strange owl; who tells Link to follow him. Link does so, and he follows the owl across the Evil Realm. The owl eventually comes across a small area around a door in a cliff where everything is green and alive as it should be. The owl tells Link that the door is the portal to the Sacred Realm, and its just powers are flowing out into the land. He tells Link that to save Surface, he must journey into the Sacred Realm. There he must pass the trials of the six goddesses of the Sacred Realm. (These trials are the quests and dungeons of the game) At the end of each quest (dungeon) he will find a sacred seal. (these are the six medallions from OoT). Link does all of this. He returns to the owl, but he finds him at the entrance of the Sacred Realm, where he suddenly turns into an old man. The old man senses that Link is curious about him and the medallions. He tells Link that he is a sage from the Sacred Realm who watches over the Surface at the behest of Hylia. He tells Link that the six medallions have little power to themselves, for Link has gained true power from the equipment and experience he gained achieving them. He tells Link that he must now journey to the Evil Realm and cleanse of its evil. Link must do this by re-uniting the Triforce and making a wish. He must first journey to Lanayru, where Zelda is being held in a deep dungeon. He tells Link she, the goddess will know Link agrees and journeys into the Evil Realm. Then he fights his way to Lanayru and saves Zelda from whatever evils the ZD put in front of him. Then Zelda tells Link that she has one piece of the Triforce, the Triforce of Wisdom. She tells Link he has the Triforce of Courage, but his piece hasn't awakened within him. She says the evil of the Evil Realm is suppressing its power. She then tells Link to journey to Faron, where he will find another evil dungeon and something to cleanse himself. Then Link escorts Zelda back to the Sacred Realm gate. He does what she asked and finally finds the Master Sword. The Master sword awakens Link's piece of the Triforce, and it glows brightly on his hand. Link then travels back to the Sacred Realm gate, where he finds the main villain has Zelda cornered. The sage tries to protect her, but he is quickly defeated. The villain then tells Link to come to his castle atop Death Mountain and get Zelda back. The sage tells Link he has to be careful and use all of his abilities, for it is clearly a trap to gather Link's Triforce. Link then courageously heads to Death Mountain and battles his way to the top. There he encounters our villain. The villain then makes declares that he will wish the Sacred Realm to become just as evil as the land of the Surface, and then we have our epic fight. At the end we have two possibilities. Ghirahim will declare that he may be finished, but evil will rise again. Ganondorf would declare that he is the very incarnation of evil, and he will rise again to haunt the world anew. Then Link gathers the pieces of the Triforce and wishes for Hyrule to be restored.
Then we have our happy little ending. Link and Zelda are saved. They store the Triforce in the Sacred Realm, for fear of what could happen if evil retrieved it again. Then Link gives the Sacred Seals back to the sage, who tells Link that he and Zelda should go forth and found a new kingdom where all the people of the world can live in peace and justice. He then tells Link to hep him think of a name. He tells Link people will love the land where the goddess Hylia rules. Then he gets it and tells Link to name it Hyrule. Then we have our ending.
Pretty solid for a first draft. Am I on to something? Questions? Comments? Concerns?